Starting phenix.real_space_refine on Fri Mar 6 11:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2r_20578/03_2026/6q2r_20578.map" } resolution = 4.3 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= 0.001 sd= 0.003 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: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 276 5.16 5 C 18868 2.51 5 N 5476 2.21 5 O 5756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "E" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "F" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "U" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "V" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "W" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "Y" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "X" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "Z" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.54, per 1000 atoms: 0.22 Number of scatterers: 30392 At special positions: 0 Unit cell: (227.91, 222.56, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 276 16.00 O 5756 8.00 N 5476 7.00 C 18868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=106, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 164 " distance=1.96 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 222 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 174 " distance=2.02 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 222 " distance=2.02 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 174 " distance=2.02 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.03 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 Simple disulfide: pdb=" SG CYS U 103 " - pdb=" SG CYS U 165 " distance=2.03 Simple disulfide: pdb=" SG CYS U 130 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 164 " - pdb=" SG CYS V 164 " distance=2.10 Simple disulfide: pdb=" SG CYS V 103 " - pdb=" SG CYS V 165 " distance=2.03 Simple disulfide: pdb=" SG CYS V 130 " - pdb=" SG CYS V 194 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 196 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 93 " distance=2.04 Simple disulfide: pdb=" SG CYS W 95 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS W 161 " - pdb=" SG CYS W 222 " distance=2.02 Simple disulfide: pdb=" SG CYS W 168 " - pdb=" SG CYS W 174 " distance=2.02 Simple disulfide: pdb=" SG CYS W 185 " - pdb=" SG CYS W 200 " distance=2.02 Simple disulfide: pdb=" SG CYS W 195 " - pdb=" SG CYS W 241 " distance=2.02 Simple disulfide: pdb=" SG CYS W 224 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 251 " - pdb=" SG CYS W 323 " distance=2.03 Simple disulfide: pdb=" SG CYS W 258 " - pdb=" SG CYS W 264 " distance=2.03 Simple disulfide: pdb=" SG CYS W 275 " - pdb=" SG CYS W 293 " distance=2.03 Simple disulfide: pdb=" SG CYS W 285 " - pdb=" SG CYS W 347 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 137 " - pdb=" SG CYS Y 142 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 197 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 166 " - pdb=" SG CYS Y 243 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 426 " - pdb=" SG CYS Y 430 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 449 " - pdb=" SG CYS Y 478 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 515 " - pdb=" SG CYS Y 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 519 " - pdb=" SG CYS Y 541 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 528 " - pdb=" SG CYS Y 558 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 565 " - pdb=" SG CYS Y 581 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 570 " - pdb=" SG CYS Y 585 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 609 " - pdb=" SG CYS Y 620 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 611 " - pdb=" SG CYS Y 618 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 93 " distance=2.04 Simple disulfide: pdb=" SG CYS X 95 " - pdb=" SG CYS X 105 " distance=2.03 Simple disulfide: pdb=" SG CYS X 161 " - pdb=" SG CYS X 222 " distance=2.02 Simple disulfide: pdb=" SG CYS X 168 " - pdb=" SG CYS X 174 " distance=2.02 Simple disulfide: pdb=" SG CYS X 185 " - pdb=" SG CYS X 200 " distance=2.02 Simple disulfide: pdb=" SG CYS X 195 " - pdb=" SG CYS X 241 " distance=2.02 Simple disulfide: pdb=" SG CYS X 224 " - pdb=" SG CYS X 229 " distance=2.03 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 323 " distance=2.03 Simple disulfide: pdb=" SG CYS X 258 " - pdb=" SG CYS X 264 " distance=2.03 Simple disulfide: pdb=" SG CYS X 275 " - pdb=" SG CYS X 293 " distance=2.03 Simple disulfide: pdb=" SG CYS X 285 " - pdb=" SG CYS X 347 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 137 " - pdb=" SG CYS Z 142 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 157 " - pdb=" SG CYS Z 197 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 166 " - pdb=" SG CYS Z 243 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 426 " - pdb=" SG CYS Z 430 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 449 " - pdb=" SG CYS Z 478 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 515 " - pdb=" SG CYS Z 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 519 " - pdb=" SG CYS Z 541 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 528 " - pdb=" SG CYS Z 558 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 565 " - pdb=" SG CYS Z 581 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 570 " - pdb=" SG CYS Z 585 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 609 " - pdb=" SG CYS Z 620 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 611 " - pdb=" SG CYS Z 618 " 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 NAG-ASN " NAG E2005 " - " ASN E 377 " " NAG E2006 " - " ASN E 394 " " NAG E2007 " - " ASN E 468 " " NAG E2008 " - " ASN E 367 " " NAG E2009 " - " ASN E 336 " " NAG E2010 " - " ASN E 361 " " NAG F2005 " - " ASN F 377 " " NAG F2006 " - " ASN F 394 " " NAG F2007 " - " ASN F 468 " " NAG F2008 " - " ASN F 367 " " NAG F2009 " - " ASN F 336 " " NAG F2010 " - " ASN F 361 " " NAG Y2005 " - " ASN Y 377 " " NAG Y2006 " - " ASN Y 394 " " NAG Y2007 " - " ASN Y 468 " " NAG Y2008 " - " ASN Y 367 " " NAG Y2009 " - " ASN Y 336 " " NAG Y2010 " - " ASN Y 361 " " NAG Z2005 " - " ASN Z 377 " " NAG Z2006 " - " ASN Z 394 " " NAG Z2007 " - " ASN Z 468 " " NAG Z2008 " - " ASN Z 367 " " NAG Z2009 " - " ASN Z 336 " " NAG Z2010 " - " ASN Z 361 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 72 sheets defined 28.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.852A pdb=" N GLY A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.678A pdb=" N LYS C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.958A pdb=" N CYS C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 Processing helix chain 'E' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.520A pdb=" N HIS E 114 " --> pdb=" O VAL E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.800A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.788A pdb=" N VAL E 521 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY E 568 " --> pdb=" O CYS E 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 564 through 568' Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 289 through 299 removed outlier: 3.957A pdb=" N CYS D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 Processing helix chain 'F' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.520A pdb=" N HIS F 114 " --> pdb=" O VAL F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.800A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.788A pdb=" N VAL F 521 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY F 568 " --> pdb=" O CYS F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 564 through 568' Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'U' and resid 113 through 116 removed outlier: 3.852A pdb=" N GLY U 116 " --> pdb=" O SER U 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 113 through 116' Processing helix chain 'U' and resid 139 through 152 Processing helix chain 'V' and resid 113 through 116 Processing helix chain 'V' and resid 139 through 151 Processing helix chain 'W' and resid 39 through 49 Processing helix chain 'W' and resid 51 through 65 Processing helix chain 'W' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE W 112 " --> pdb=" O ILE W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 170 Processing helix chain 'W' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS W 175 " --> pdb=" O ASN W 171 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS W 200 " --> pdb=" O ASN W 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR W 216 " --> pdb=" O PRO W 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG W 218 " --> pdb=" O GLU W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA W 230 " --> pdb=" O ASP W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 238 No H-bonds generated for 'chain 'W' and resid 236 through 238' Processing helix chain 'W' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP W 261 " --> pdb=" O VAL W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 261 through 275 removed outlier: 3.566A pdb=" N ASN W 274 " --> pdb=" O ASP W 270 " (cutoff:3.500A) Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 299 removed outlier: 3.958A pdb=" N CYS W 293 " --> pdb=" O ASN W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP W 341 " --> pdb=" O LYS W 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 357 Processing helix chain 'Y' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP Y 106 " --> pdb=" O ASP Y 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 114 removed outlier: 3.521A pdb=" N HIS Y 114 " --> pdb=" O VAL Y 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 111 through 114' Processing helix chain 'Y' and resid 162 through 167 removed outlier: 3.799A pdb=" N PHE Y 167 " --> pdb=" O ARG Y 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 197 Processing helix chain 'Y' and resid 309 through 313 Processing helix chain 'Y' and resid 322 through 328 Processing helix chain 'Y' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA Y 432 " --> pdb=" O ASN Y 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE Y 433 " --> pdb=" O CYS Y 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 429 through 433' Processing helix chain 'Y' and resid 470 through 475 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.789A pdb=" N VAL Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 525 through 530 Processing helix chain 'Y' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP Y 567 " --> pdb=" O THR Y 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY Y 568 " --> pdb=" O CYS Y 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 564 through 568' Processing helix chain 'Y' and resid 581 through 586 Processing helix chain 'X' and resid 39 through 49 Processing helix chain 'X' and resid 51 through 65 Processing helix chain 'X' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE X 112 " --> pdb=" O ILE X 108 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 170 Processing helix chain 'X' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS X 175 " --> pdb=" O ASN X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS X 200 " --> pdb=" O ASN X 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR X 216 " --> pdb=" O PRO X 212 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG X 218 " --> pdb=" O GLU X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA X 230 " --> pdb=" O ASP X 226 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 238 No H-bonds generated for 'chain 'X' and resid 236 through 238' Processing helix chain 'X' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP X 261 " --> pdb=" O VAL X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN X 274 " --> pdb=" O ASP X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 285 through 288 Processing helix chain 'X' and resid 289 through 299 removed outlier: 3.959A pdb=" N CYS X 293 " --> pdb=" O ASN X 289 " (cutoff:3.500A) Processing helix chain 'X' and resid 331 through 344 removed outlier: 3.724A pdb=" N ASP X 341 " --> pdb=" O LYS X 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE X 342 " --> pdb=" O PHE X 338 " (cutoff:3.500A) Processing helix chain 'X' and resid 345 through 357 Processing helix chain 'Z' and resid 102 through 110 removed outlier: 4.133A pdb=" N TRP Z 106 " --> pdb=" O ASP Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 114 removed outlier: 3.521A pdb=" N HIS Z 114 " --> pdb=" O VAL Z 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 111 through 114' Processing helix chain 'Z' and resid 162 through 167 removed outlier: 3.799A pdb=" N PHE Z 167 " --> pdb=" O ARG Z 163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 197 Processing helix chain 'Z' and resid 309 through 313 Processing helix chain 'Z' and resid 322 through 328 Processing helix chain 'Z' and resid 429 through 433 removed outlier: 3.878A pdb=" N ALA Z 432 " --> pdb=" O ASN Z 429 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE Z 433 " --> pdb=" O CYS Z 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 429 through 433' Processing helix chain 'Z' and resid 470 through 475 Processing helix chain 'Z' and resid 518 through 522 removed outlier: 3.789A pdb=" N VAL Z 521 " --> pdb=" O SER Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 525 through 530 Processing helix chain 'Z' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP Z 567 " --> pdb=" O THR Z 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY Z 568 " --> pdb=" O CYS Z 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 564 through 568' Processing helix chain 'Z' and resid 581 through 586 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111 Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.694A pdb=" N LEU E 95 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.824A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE E 174 " --> pdb=" O PRO E 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR E 261 " --> pdb=" O PHE E 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 280 through 283 Processing sheet with id=AB7, first strand: chain 'E' and resid 292 through 300 removed outlier: 6.349A pdb=" N LEU E 356 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR E 295 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 354 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG E 297 " --> pdb=" O HIS E 352 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS E 352 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE E 299 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR E 350 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 410 through 413 removed outlier: 7.547A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 486 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AC2, first strand: chain 'E' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'E' and resid 595 through 596 Processing sheet with id=AC4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.695A pdb=" N LEU F 95 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.824A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE F 174 " --> pdb=" O PRO F 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 261 " --> pdb=" O PHE F 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 280 through 283 Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 300 removed outlier: 6.350A pdb=" N LEU F 356 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR F 295 " --> pdb=" O TYR F 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR F 354 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG F 297 " --> pdb=" O HIS F 352 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS F 352 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE F 299 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR F 350 " --> pdb=" O PHE F 299 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 410 through 413 removed outlier: 7.546A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 486 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 589 through 591 Processing sheet with id=AD9, first strand: chain 'F' and resid 595 through 596 Processing sheet with id=AE1, first strand: chain 'U' and resid 104 through 111 Processing sheet with id=AE2, first strand: chain 'U' and resid 165 through 167 Processing sheet with id=AE3, first strand: chain 'U' and resid 173 through 177 Processing sheet with id=AE4, first strand: chain 'V' and resid 104 through 111 Processing sheet with id=AE5, first strand: chain 'V' and resid 165 through 167 Processing sheet with id=AE6, first strand: chain 'V' and resid 173 through 177 Processing sheet with id=AE7, first strand: chain 'W' and resid 308 through 309 Processing sheet with id=AE8, first strand: chain 'Y' and resid 30 through 31 Processing sheet with id=AE9, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Y 36 " --> pdb=" O TYR Y 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Y 148 " --> pdb=" O TYR Y 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Y 36 " --> pdb=" O TYR Y 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Y 148 " --> pdb=" O TYR Y 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 49 through 52 removed outlier: 6.695A pdb=" N LEU Y 95 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 72 through 73 removed outlier: 3.823A pdb=" N HIS Y 81 " --> pdb=" O LEU Y 72 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE Y 174 " --> pdb=" O PRO Y 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR Y 261 " --> pdb=" O PHE Y 174 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR Y 184 " --> pdb=" O THR Y 225 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR Y 225 " --> pdb=" O THR Y 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS Y 186 " --> pdb=" O VAL Y 223 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 280 through 283 Processing sheet with id=AF7, first strand: chain 'Y' and resid 292 through 300 removed outlier: 6.350A pdb=" N LEU Y 356 " --> pdb=" O VAL Y 293 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR Y 295 " --> pdb=" O TYR Y 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR Y 354 " --> pdb=" O THR Y 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG Y 297 " --> pdb=" O HIS Y 352 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS Y 352 " --> pdb=" O ARG Y 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE Y 299 " --> pdb=" O THR Y 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR Y 350 " --> pdb=" O PHE Y 299 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 410 through 413 removed outlier: 7.548A pdb=" N LEU Y 410 " --> pdb=" O THR Y 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU Y 505 " --> pdb=" O LEU Y 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL Y 412 " --> pdb=" O GLU Y 505 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL Y 486 " --> pdb=" O LYS Y 441 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN Y 421 " --> pdb=" O VAL Y 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL Y 467 " --> pdb=" O GLN Y 421 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY Y 423 " --> pdb=" O LEU Y 465 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 542 through 544 Processing sheet with id=AG2, first strand: chain 'Y' and resid 589 through 591 Processing sheet with id=AG3, first strand: chain 'Y' and resid 595 through 596 Processing sheet with id=AG4, first strand: chain 'X' and resid 308 through 309 Processing sheet with id=AG5, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AG6, first strand: chain 'Z' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Z 36 " --> pdb=" O TYR Z 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Z 148 " --> pdb=" O TYR Z 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Z 36 " --> pdb=" O TYR Z 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Z 148 " --> pdb=" O TYR Z 36 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 49 through 52 removed outlier: 6.694A pdb=" N LEU Z 95 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 72 through 73 removed outlier: 3.823A pdb=" N HIS Z 81 " --> pdb=" O LEU Z 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 174 through 176 removed outlier: 3.877A pdb=" N PHE Z 174 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR Z 261 " --> pdb=" O PHE Z 174 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 184 through 187 removed outlier: 6.669A pdb=" N THR Z 184 " --> pdb=" O THR Z 225 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR Z 225 " --> pdb=" O THR Z 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS Z 186 " --> pdb=" O VAL Z 223 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 280 through 283 Processing sheet with id=AH4, first strand: chain 'Z' and resid 292 through 300 removed outlier: 6.351A pdb=" N LEU Z 356 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR Z 295 " --> pdb=" O TYR Z 354 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR Z 354 " --> pdb=" O THR Z 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG Z 297 " --> pdb=" O HIS Z 352 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS Z 352 " --> pdb=" O ARG Z 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE Z 299 " --> pdb=" O THR Z 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR Z 350 " --> pdb=" O PHE Z 299 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 410 through 413 removed outlier: 7.548A pdb=" N LEU Z 410 " --> pdb=" O THR Z 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU Z 505 " --> pdb=" O LEU Z 410 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL Z 412 " --> pdb=" O GLU Z 505 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Z 486 " --> pdb=" O LYS Z 441 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN Z 421 " --> pdb=" O VAL Z 467 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL Z 467 " --> pdb=" O GLN Z 421 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY Z 423 " --> pdb=" O LEU Z 465 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 542 through 544 Processing sheet with id=AH8, first strand: chain 'Z' and resid 589 through 591 Processing sheet with id=AH9, first strand: chain 'Z' and resid 595 through 596 1004 hydrogen bonds defined for protein. 2778 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: 5.82 Time building geometry restraints manager: 2.92 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: 10281 1.34 - 1.46: 7183 1.46 - 1.59: 13236 1.59 - 1.71: 0 1.71 - 1.83: 308 Bond restraints: 31008 Sorted by residual: bond pdb=" C CYS Z 565 " pdb=" N PRO Z 566 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.75e+00 bond pdb=" C CYS Y 565 " pdb=" N PRO Y 566 " ideal model delta sigma weight residual 1.334 1.389 -0.056 2.34e-02 1.83e+03 5.64e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.62e+00 bond pdb=" C CYS E 565 " pdb=" N PRO E 566 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.60e+00 bond pdb=" C1 NAG F2005 " pdb=" O5 NAG F2005 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 ... (remaining 31003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 38873 1.44 - 2.88: 2685 2.88 - 4.33: 293 4.33 - 5.77: 80 5.77 - 7.21: 61 Bond angle restraints: 41992 Sorted by residual: angle pdb=" N VAL Z 303 " pdb=" CA VAL Z 303 " pdb=" C VAL Z 303 " ideal model delta sigma weight residual 113.53 107.00 6.53 9.80e-01 1.04e+00 4.44e+01 angle pdb=" N VAL Y 303 " pdb=" CA VAL Y 303 " pdb=" C VAL Y 303 " ideal model delta sigma weight residual 113.53 107.02 6.51 9.80e-01 1.04e+00 4.41e+01 angle pdb=" N VAL F 303 " pdb=" CA VAL F 303 " pdb=" C VAL F 303 " ideal model delta sigma weight residual 113.53 107.03 6.50 9.80e-01 1.04e+00 4.40e+01 angle pdb=" N VAL E 303 " pdb=" CA VAL E 303 " pdb=" C VAL E 303 " ideal model delta sigma weight residual 113.53 107.05 6.48 9.80e-01 1.04e+00 4.38e+01 angle pdb=" N ASN Y 448 " pdb=" CA ASN Y 448 " pdb=" C ASN Y 448 " ideal model delta sigma weight residual 114.75 109.97 4.78 1.26e+00 6.30e-01 1.44e+01 ... (remaining 41987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 18661 16.02 - 32.05: 579 32.05 - 48.07: 174 48.07 - 64.10: 18 64.10 - 80.12: 22 Dihedral angle restraints: 19454 sinusoidal: 8346 harmonic: 11108 Sorted by residual: dihedral pdb=" CB CYS Z 426 " pdb=" SG CYS Z 426 " pdb=" SG CYS Z 430 " pdb=" CB CYS Z 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.12 80.12 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS Y 426 " pdb=" SG CYS Y 426 " pdb=" SG CYS Y 430 " pdb=" CB CYS Y 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.11 80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.10 80.10 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 19451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2647 0.034 - 0.069: 1329 0.069 - 0.103: 455 0.103 - 0.137: 185 0.137 - 0.172: 32 Chirality restraints: 4648 Sorted by residual: chirality pdb=" CB VAL Z 340 " pdb=" CA VAL Z 340 " pdb=" CG1 VAL Z 340 " pdb=" CG2 VAL Z 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB VAL Y 340 " pdb=" CA VAL Y 340 " pdb=" CG1 VAL Y 340 " pdb=" CG2 VAL Y 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CB VAL E 340 " pdb=" CA VAL E 340 " pdb=" CG1 VAL E 340 " pdb=" CG2 VAL E 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 4645 not shown) Planarity restraints: 5524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 320 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO D 321 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 320 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO W 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO W 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO W 321 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 320 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO C 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.028 5.00e-02 4.00e+02 ... (remaining 5521 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 28 2.09 - 2.79: 7103 2.79 - 3.49: 37315 3.49 - 4.20: 68052 4.20 - 4.90: 114948 Nonbonded interactions: 227446 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.384 3.040 nonbonded pdb=" OD2 ASP Y 300 " pdb=" OH TYR Y 314 " model vdw 1.384 3.040 nonbonded pdb=" OD2 ASP Z 300 " pdb=" OH TYR Z 314 " model vdw 1.384 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.384 3.040 nonbonded pdb=" OD1 ASP Y 230 " pdb=" OE1 GLU Y 232 " model vdw 1.698 3.040 ... (remaining 227441 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 26.080 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 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 0.071 31138 Z= 0.224 Angle : 0.831 7.209 42276 Z= 0.480 Chirality : 0.048 0.172 4648 Planarity : 0.006 0.052 5500 Dihedral : 8.755 76.248 11936 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.85 (0.11), residues: 3720 helix: -2.84 (0.11), residues: 888 sheet: -1.79 (0.16), residues: 944 loop : -2.82 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 101 TYR 0.021 0.002 TYR D 181 PHE 0.019 0.002 PHE E 188 TRP 0.026 0.003 TRP Y 334 HIS 0.007 0.001 HIS X 201 Details of bonding type rmsd covalent geometry : bond 0.00446 (31008) covalent geometry : angle 0.82284 (41992) SS BOND : bond 0.01045 ( 106) SS BOND : angle 1.19018 ( 212) hydrogen bonds : bond 0.16381 ( 1004) hydrogen bonds : angle 7.08377 ( 2778) link_NAG-ASN : bond 0.00326 ( 24) link_NAG-ASN : angle 2.50709 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.214 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 252 LEU cc_start: 0.7609 (mt) cc_final: 0.7261 (pp) REVERT: F 34 ASP cc_start: 0.7316 (p0) cc_final: 0.6443 (t70) REVERT: F 86 ILE cc_start: 0.7831 (mt) cc_final: 0.7081 (mt) REVERT: W 201 HIS cc_start: 0.5672 (m170) cc_final: 0.5461 (m170) REVERT: W 207 PHE cc_start: 0.7581 (t80) cc_final: 0.7254 (t80) REVERT: W 248 LYS cc_start: 0.7817 (mttt) cc_final: 0.7561 (mmtt) REVERT: X 331 MET cc_start: 0.5911 (mmt) cc_final: 0.5530 (mmm) REVERT: Z 295 THR cc_start: 0.7134 (m) cc_final: 0.6516 (p) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.2497 time to fit residues: 209.0128 Evaluate side-chains 202 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN E 246 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS D 107 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 HIS F 482 HIS F 554 ASN W 274 ASN W 330 ASN Y 246 HIS ** Y 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 HIS Z 103 HIS ** Z 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 443 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.075242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.062155 restraints weight = 311264.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.064293 restraints weight = 197115.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.064573 restraints weight = 121566.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.065243 restraints weight = 98836.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.065489 restraints weight = 81880.654| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31138 Z= 0.179 Angle : 0.679 11.599 42276 Z= 0.349 Chirality : 0.042 0.230 4648 Planarity : 0.006 0.078 5500 Dihedral : 5.793 42.737 4756 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.63 (0.12), residues: 3720 helix: -0.99 (0.15), residues: 904 sheet: -1.47 (0.16), residues: 948 loop : -2.28 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 297 TYR 0.037 0.002 TYR B 170 PHE 0.021 0.002 PHE E 174 TRP 0.033 0.002 TRP Z 37 HIS 0.018 0.001 HIS Z 114 Details of bonding type rmsd covalent geometry : bond 0.00385 (31008) covalent geometry : angle 0.66945 (41992) SS BOND : bond 0.00301 ( 106) SS BOND : angle 1.11163 ( 212) hydrogen bonds : bond 0.03658 ( 1004) hydrogen bonds : angle 5.58486 ( 2778) link_NAG-ASN : bond 0.00982 ( 24) link_NAG-ASN : angle 2.30289 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.291 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: C 335 CYS cc_start: 0.7079 (t) cc_final: 0.6866 (t) REVERT: E 72 LEU cc_start: 0.8579 (tp) cc_final: 0.8245 (tp) REVERT: D 237 ILE cc_start: 0.8388 (pt) cc_final: 0.7869 (tp) REVERT: D 308 ASN cc_start: 0.8722 (t0) cc_final: 0.8414 (m-40) REVERT: W 201 HIS cc_start: 0.7201 (m170) cc_final: 0.6921 (m170) REVERT: W 331 MET cc_start: 0.8632 (mpp) cc_final: 0.8364 (mpp) REVERT: W 335 CYS cc_start: 0.7347 (t) cc_final: 0.6885 (t) REVERT: Y 72 LEU cc_start: 0.8552 (tp) cc_final: 0.8217 (tp) REVERT: Z 38 GLU cc_start: 0.7454 (tp30) cc_final: 0.7216 (tt0) REVERT: Z 85 TRP cc_start: 0.5359 (m-90) cc_final: 0.5096 (m100) REVERT: Z 341 GLN cc_start: 0.5441 (pm20) cc_final: 0.4945 (tt0) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2116 time to fit residues: 84.2695 Evaluate side-chains 130 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 83 optimal weight: 20.0000 chunk 351 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 chunk 324 optimal weight: 40.0000 chunk 203 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 285 optimal weight: 0.0000 chunk 233 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 165 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 343 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN D 62 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 262 HIS ** W 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 326 GLN Y 333 HIS ** Y 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 HIS Z 187 GLN ** Z 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 545 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.069006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.056278 restraints weight = 315652.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.057660 restraints weight = 193196.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.058568 restraints weight = 132650.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.059156 restraints weight = 100029.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.059634 restraints weight = 81488.678| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31138 Z= 0.227 Angle : 0.768 11.213 42276 Z= 0.398 Chirality : 0.046 0.253 4648 Planarity : 0.007 0.119 5500 Dihedral : 6.305 44.201 4756 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.31 % Rotamer: Outliers : 0.24 % Allowed : 3.07 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.33 (0.13), residues: 3720 helix: -0.55 (0.16), residues: 928 sheet: -1.23 (0.16), residues: 960 loop : -2.25 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG A 111 TYR 0.030 0.002 TYR V 170 PHE 0.028 0.003 PHE F 174 TRP 0.039 0.003 TRP F 139 HIS 0.014 0.002 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00480 (31008) covalent geometry : angle 0.75900 (41992) SS BOND : bond 0.00458 ( 106) SS BOND : angle 1.36797 ( 212) hydrogen bonds : bond 0.04363 ( 1004) hydrogen bonds : angle 5.93515 ( 2778) link_NAG-ASN : bond 0.00564 ( 24) link_NAG-ASN : angle 2.18305 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 1.275 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: C 219 MET cc_start: 0.7905 (ppp) cc_final: 0.7507 (ppp) REVERT: D 331 MET cc_start: 0.7389 (tpp) cc_final: 0.7148 (tpt) REVERT: F 67 ARG cc_start: 0.7330 (mtm180) cc_final: 0.7118 (tpm170) REVERT: F 263 TYR cc_start: 0.8213 (m-10) cc_final: 0.7991 (m-80) REVERT: F 480 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7097 (tp30) REVERT: W 162 LEU cc_start: 0.8332 (tt) cc_final: 0.8044 (tt) REVERT: W 219 MET cc_start: 0.7824 (ppp) cc_final: 0.7553 (ppp) REVERT: W 305 MET cc_start: 0.8420 (tpt) cc_final: 0.8026 (mmm) REVERT: W 331 MET cc_start: 0.8912 (mpp) cc_final: 0.8607 (mpp) REVERT: X 58 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7416 (ptp-170) REVERT: X 305 MET cc_start: 0.7027 (ttt) cc_final: 0.6426 (ttt) REVERT: Z 38 GLU cc_start: 0.8367 (tp30) cc_final: 0.7626 (tt0) REVERT: Z 85 TRP cc_start: 0.5457 (m-90) cc_final: 0.5184 (m100) outliers start: 8 outliers final: 1 residues processed: 202 average time/residue: 0.2062 time to fit residues: 65.4763 Evaluate side-chains 110 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 212 optimal weight: 20.0000 chunk 36 optimal weight: 0.0570 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 153 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 325 optimal weight: 30.0000 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 254 optimal weight: 50.0000 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN E 482 HIS D 62 GLN D 201 HIS F 114 HIS F 333 HIS W 330 ASN Y 482 HIS X 272 HIS X 308 ASN X 330 ASN Z 187 GLN Z 333 HIS Z 482 HIS Z 545 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.070539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057488 restraints weight = 313539.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.058987 restraints weight = 186705.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.059962 restraints weight = 126118.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.060494 restraints weight = 93852.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.061054 restraints weight = 76750.646| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 31138 Z= 0.101 Angle : 0.557 12.011 42276 Z= 0.281 Chirality : 0.041 0.219 4648 Planarity : 0.004 0.049 5500 Dihedral : 5.121 40.018 4756 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.79 (0.13), residues: 3720 helix: 0.08 (0.17), residues: 944 sheet: -1.03 (0.16), residues: 976 loop : -1.97 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 111 TYR 0.026 0.001 TYR V 170 PHE 0.012 0.001 PHE Z 188 TRP 0.019 0.001 TRP F 85 HIS 0.012 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00224 (31008) covalent geometry : angle 0.54957 (41992) SS BOND : bond 0.00204 ( 106) SS BOND : angle 0.99889 ( 212) hydrogen bonds : bond 0.03082 ( 1004) hydrogen bonds : angle 5.24266 ( 2778) link_NAG-ASN : bond 0.00201 ( 24) link_NAG-ASN : angle 1.67631 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.267 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: C 331 MET cc_start: 0.8463 (mpp) cc_final: 0.8072 (mpp) REVERT: F 239 LEU cc_start: 0.4264 (mm) cc_final: 0.3876 (pp) REVERT: F 370 MET cc_start: 0.6060 (tpt) cc_final: 0.5722 (tpp) REVERT: V 183 TYR cc_start: 0.7302 (m-80) cc_final: 0.6740 (m-10) REVERT: W 181 TYR cc_start: 0.7247 (p90) cc_final: 0.7039 (p90) REVERT: W 305 MET cc_start: 0.8382 (tpt) cc_final: 0.8124 (mmm) REVERT: W 331 MET cc_start: 0.8904 (mpp) cc_final: 0.8565 (mpp) REVERT: Z 38 GLU cc_start: 0.8093 (tp30) cc_final: 0.7353 (tt0) REVERT: Z 85 TRP cc_start: 0.5559 (m-90) cc_final: 0.5123 (m100) outliers start: 3 outliers final: 0 residues processed: 177 average time/residue: 0.2065 time to fit residues: 57.9251 Evaluate side-chains 105 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 106 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 246 optimal weight: 30.0000 chunk 141 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 103 HIS E 138 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN E 343 ASN E 403 HIS D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 330 ASN F 114 HIS F 327 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN F 499 GLN W 330 ASN Y 84 ASN Y 103 HIS Y 138 GLN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 HIS ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 187 GLN ** Z 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.065511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.053558 restraints weight = 313283.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.054819 restraints weight = 190438.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.055633 restraints weight = 130145.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.056214 restraints weight = 98985.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.056592 restraints weight = 80685.637| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.8712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 31138 Z= 0.232 Angle : 0.791 11.861 42276 Z= 0.404 Chirality : 0.046 0.262 4648 Planarity : 0.007 0.099 5500 Dihedral : 6.466 46.264 4756 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.15 % Allowed : 2.80 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.14 (0.13), residues: 3720 helix: -0.44 (0.16), residues: 920 sheet: -1.24 (0.16), residues: 988 loop : -2.02 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG U 139 TYR 0.025 0.002 TYR Z 146 PHE 0.022 0.003 PHE Z 433 TRP 0.043 0.003 TRP Y 334 HIS 0.018 0.002 HIS Z 333 Details of bonding type rmsd covalent geometry : bond 0.00498 (31008) covalent geometry : angle 0.78047 (41992) SS BOND : bond 0.00424 ( 106) SS BOND : angle 1.52798 ( 212) hydrogen bonds : bond 0.04455 ( 1004) hydrogen bonds : angle 6.28390 ( 2778) link_NAG-ASN : bond 0.00342 ( 24) link_NAG-ASN : angle 2.38026 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 1.161 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: C 201 HIS cc_start: 0.7847 (m170) cc_final: 0.7634 (m90) REVERT: C 305 MET cc_start: 0.7833 (mmm) cc_final: 0.7599 (mmm) REVERT: C 331 MET cc_start: 0.8690 (mpp) cc_final: 0.8184 (mpp) REVERT: E 138 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7924 (pp30) REVERT: D 331 MET cc_start: 0.7632 (tpt) cc_final: 0.7127 (tpp) REVERT: F 263 TYR cc_start: 0.8371 (m-10) cc_final: 0.8134 (m-80) REVERT: F 370 MET cc_start: 0.6211 (tpt) cc_final: 0.5937 (tpp) REVERT: F 484 MET cc_start: 0.8005 (mmm) cc_final: 0.7626 (tpt) REVERT: W 300 MET cc_start: 0.8267 (mmt) cc_final: 0.8012 (mmt) REVERT: W 305 MET cc_start: 0.8392 (tpt) cc_final: 0.8173 (mmm) REVERT: W 331 MET cc_start: 0.8794 (mpp) cc_final: 0.8501 (mpp) REVERT: Y 138 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: X 331 MET cc_start: 0.6559 (tpt) cc_final: 0.6174 (tpt) REVERT: Z 38 GLU cc_start: 0.8503 (tp30) cc_final: 0.7805 (tt0) REVERT: Z 85 TRP cc_start: 0.5512 (m-90) cc_final: 0.5144 (m100) REVERT: Z 117 PRO cc_start: -0.0438 (Cg_endo) cc_final: -0.1593 (Cg_exo) outliers start: 5 outliers final: 1 residues processed: 166 average time/residue: 0.1981 time to fit residues: 52.9342 Evaluate side-chains 103 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 239 optimal weight: 0.1980 chunk 177 optimal weight: 50.0000 chunk 264 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 62 optimal weight: 50.0000 chunk 372 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 201 HIS W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 187 GLN ** Z 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.066264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.054489 restraints weight = 314455.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.055752 restraints weight = 187536.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.056550 restraints weight = 126679.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.057139 restraints weight = 95772.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057541 restraints weight = 78149.405| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.8931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31138 Z= 0.133 Angle : 0.605 12.660 42276 Z= 0.307 Chirality : 0.042 0.205 4648 Planarity : 0.005 0.054 5500 Dihedral : 5.626 42.700 4756 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.06 % Allowed : 1.02 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.80 (0.13), residues: 3720 helix: 0.07 (0.17), residues: 928 sheet: -1.21 (0.16), residues: 944 loop : -1.85 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Z 414 TYR 0.016 0.001 TYR V 170 PHE 0.021 0.001 PHE Z 31 TRP 0.039 0.002 TRP E 334 HIS 0.010 0.001 HIS Z 333 Details of bonding type rmsd covalent geometry : bond 0.00288 (31008) covalent geometry : angle 0.59662 (41992) SS BOND : bond 0.00261 ( 106) SS BOND : angle 1.11082 ( 212) hydrogen bonds : bond 0.03303 ( 1004) hydrogen bonds : angle 5.60357 ( 2778) link_NAG-ASN : bond 0.00231 ( 24) link_NAG-ASN : angle 1.97795 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 TYR cc_start: 0.6718 (m-80) cc_final: 0.6406 (m-10) REVERT: C 305 MET cc_start: 0.7587 (mmm) cc_final: 0.7145 (mmt) REVERT: C 331 MET cc_start: 0.8646 (mpp) cc_final: 0.8195 (mpp) REVERT: D 331 MET cc_start: 0.7853 (mmm) cc_final: 0.7603 (tpp) REVERT: F 370 MET cc_start: 0.6652 (tpt) cc_final: 0.6399 (tpp) REVERT: W 181 TYR cc_start: 0.7707 (p90) cc_final: 0.7217 (p90) REVERT: W 300 MET cc_start: 0.8047 (mmt) cc_final: 0.7838 (mmt) REVERT: W 305 MET cc_start: 0.8451 (tpt) cc_final: 0.8243 (mmm) REVERT: W 331 MET cc_start: 0.8686 (mpp) cc_final: 0.8450 (mpp) REVERT: Z 38 GLU cc_start: 0.8390 (tp30) cc_final: 0.7715 (tt0) REVERT: Z 85 TRP cc_start: 0.5507 (m-90) cc_final: 0.4893 (m100) REVERT: Z 484 MET cc_start: 0.5419 (pmm) cc_final: 0.4972 (pmm) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.1925 time to fit residues: 50.5988 Evaluate side-chains 102 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 305 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 243 optimal weight: 40.0000 chunk 261 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 328 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 201 HIS ** W 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 187 GLN Z 437 ASN ** Z 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.063880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.052480 restraints weight = 313370.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.053665 restraints weight = 188069.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.054409 restraints weight = 128412.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.054883 restraints weight = 97080.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.055267 restraints weight = 79861.247| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.9885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31138 Z= 0.184 Angle : 0.682 12.276 42276 Z= 0.346 Chirality : 0.043 0.206 4648 Planarity : 0.006 0.065 5500 Dihedral : 5.970 42.889 4756 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.06 % Allowed : 1.35 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.94 (0.13), residues: 3720 helix: -0.11 (0.17), residues: 924 sheet: -1.22 (0.16), residues: 988 loop : -1.94 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 111 TYR 0.030 0.002 TYR V 183 PHE 0.019 0.002 PHE F 433 TRP 0.032 0.002 TRP E 334 HIS 0.012 0.001 HIS Z 333 Details of bonding type rmsd covalent geometry : bond 0.00396 (31008) covalent geometry : angle 0.67332 (41992) SS BOND : bond 0.00312 ( 106) SS BOND : angle 1.09791 ( 212) hydrogen bonds : bond 0.03789 ( 1004) hydrogen bonds : angle 5.92724 ( 2778) link_NAG-ASN : bond 0.00303 ( 24) link_NAG-ASN : angle 2.18147 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 MET cc_start: 0.7888 (mmm) cc_final: 0.7518 (mmt) REVERT: C 331 MET cc_start: 0.8844 (mpp) cc_final: 0.8383 (mpp) REVERT: E 511 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7188 (mt-10) REVERT: F 263 TYR cc_start: 0.8421 (m-10) cc_final: 0.8200 (m-80) REVERT: W 99 MET cc_start: 0.7985 (ptt) cc_final: 0.6677 (ppp) REVERT: W 181 TYR cc_start: 0.8002 (p90) cc_final: 0.7488 (p90) REVERT: W 300 MET cc_start: 0.8157 (mmt) cc_final: 0.7942 (mmt) REVERT: Y 511 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7204 (mt-10) REVERT: Z 85 TRP cc_start: 0.5667 (m-90) cc_final: 0.5330 (m100) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.1832 time to fit residues: 41.8149 Evaluate side-chains 95 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 84 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 326 optimal weight: 30.0000 chunk 333 optimal weight: 9.9990 chunk 168 optimal weight: 50.0000 chunk 61 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN C 262 HIS E 81 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 201 HIS W 250 ASN W 330 ASN Y 81 HIS ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 HIS X 159 ASN X 262 HIS ** X 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 330 ASN Z 187 GLN ** Z 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 594 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.061410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.050222 restraints weight = 316731.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.051355 restraints weight = 189146.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.052170 restraints weight = 128800.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.052705 restraints weight = 96403.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.052996 restraints weight = 78403.650| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 1.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31138 Z= 0.231 Angle : 0.777 11.903 42276 Z= 0.397 Chirality : 0.046 0.226 4648 Planarity : 0.006 0.070 5500 Dihedral : 6.635 46.211 4756 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.32 (0.13), residues: 3720 helix: -0.52 (0.16), residues: 928 sheet: -1.37 (0.16), residues: 948 loop : -2.17 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG Z 180 TYR 0.036 0.002 TYR B 183 PHE 0.026 0.002 PHE F 433 TRP 0.033 0.003 TRP E 334 HIS 0.023 0.002 HIS F 103 Details of bonding type rmsd covalent geometry : bond 0.00491 (31008) covalent geometry : angle 0.76684 (41992) SS BOND : bond 0.00594 ( 106) SS BOND : angle 1.28370 ( 212) hydrogen bonds : bond 0.04351 ( 1004) hydrogen bonds : angle 6.49941 ( 2778) link_NAG-ASN : bond 0.00372 ( 24) link_NAG-ASN : angle 2.56226 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 TYR cc_start: 0.7198 (m-80) cc_final: 0.6959 (m-10) REVERT: C 305 MET cc_start: 0.7894 (mmm) cc_final: 0.7468 (mmt) REVERT: C 331 MET cc_start: 0.8909 (mpp) cc_final: 0.8520 (mpp) REVERT: E 511 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 284 SER cc_start: 0.8766 (m) cc_final: 0.8556 (t) REVERT: D 300 MET cc_start: 0.6705 (mmp) cc_final: 0.6428 (mmm) REVERT: D 331 MET cc_start: 0.7541 (tpp) cc_final: 0.7288 (tpp) REVERT: F 122 TYR cc_start: 0.8549 (p90) cc_final: 0.8232 (p90) REVERT: F 480 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6490 (tp30) REVERT: W 253 ASP cc_start: 0.8286 (m-30) cc_final: 0.8056 (m-30) REVERT: W 300 MET cc_start: 0.8154 (mmt) cc_final: 0.7946 (mmt) REVERT: Y 511 GLU cc_start: 0.8078 (mt-10) cc_final: 0.6722 (mt-10) REVERT: X 107 GLN cc_start: 0.7456 (mt0) cc_final: 0.7195 (pp30) REVERT: Z 85 TRP cc_start: 0.5956 (m-90) cc_final: 0.5568 (m100) REVERT: Z 563 LYS cc_start: 0.8250 (tmtt) cc_final: 0.7911 (pptt) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.1830 time to fit residues: 39.8439 Evaluate side-chains 95 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 160 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 137 optimal weight: 0.0170 chunk 337 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS C 272 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN D 62 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 272 HIS D 330 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 272 HIS Z 187 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.063506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.052157 restraints weight = 314391.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.053305 restraints weight = 186731.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.053967 restraints weight = 127673.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054657 restraints weight = 99023.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 77)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.055057 restraints weight = 79676.290| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 1.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31138 Z= 0.113 Angle : 0.602 12.839 42276 Z= 0.303 Chirality : 0.043 0.198 4648 Planarity : 0.005 0.062 5500 Dihedral : 5.566 44.107 4756 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 3720 helix: 0.12 (0.17), residues: 928 sheet: -1.13 (0.17), residues: 908 loop : -1.88 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 178 TYR 0.014 0.001 TYR V 183 PHE 0.012 0.001 PHE F 433 TRP 0.029 0.002 TRP F 85 HIS 0.007 0.001 HIS Z 333 Details of bonding type rmsd covalent geometry : bond 0.00248 (31008) covalent geometry : angle 0.59375 (41992) SS BOND : bond 0.00235 ( 106) SS BOND : angle 1.13762 ( 212) hydrogen bonds : bond 0.03269 ( 1004) hydrogen bonds : angle 5.63615 ( 2778) link_NAG-ASN : bond 0.00268 ( 24) link_NAG-ASN : angle 1.81761 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 TYR cc_start: 0.6695 (m-80) cc_final: 0.6286 (m-10) REVERT: C 305 MET cc_start: 0.7682 (mmm) cc_final: 0.7154 (mmt) REVERT: C 331 MET cc_start: 0.8840 (mpp) cc_final: 0.8362 (mpp) REVERT: E 511 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7273 (mt-10) REVERT: D 103 LEU cc_start: 0.5536 (tp) cc_final: 0.5302 (pt) REVERT: D 300 MET cc_start: 0.6593 (mmp) cc_final: 0.6232 (mmm) REVERT: Y 511 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7426 (mt-10) REVERT: X 107 GLN cc_start: 0.7526 (mt0) cc_final: 0.7321 (pp30) REVERT: X 305 MET cc_start: 0.7388 (ttt) cc_final: 0.7158 (ttm) REVERT: Z 85 TRP cc_start: 0.5864 (m-90) cc_final: 0.5552 (m100) REVERT: Z 563 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7917 (pptt) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.1892 time to fit residues: 45.8596 Evaluate side-chains 92 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 223 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 361 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 349 optimal weight: 40.0000 chunk 269 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN D 62 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 272 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 187 GLN ** Z 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.061748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.050631 restraints weight = 315372.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.051775 restraints weight = 190116.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.052420 restraints weight = 129950.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.053053 restraints weight = 100235.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.053392 restraints weight = 81408.658| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 1.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31138 Z= 0.171 Angle : 0.668 13.219 42276 Z= 0.339 Chirality : 0.044 0.222 4648 Planarity : 0.005 0.069 5500 Dihedral : 5.855 42.074 4756 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.09 % Allowed : 0.24 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.92 (0.13), residues: 3720 helix: -0.06 (0.17), residues: 924 sheet: -1.19 (0.17), residues: 968 loop : -1.94 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 175 TYR 0.022 0.002 TYR V 183 PHE 0.018 0.002 PHE D 221 TRP 0.025 0.002 TRP E 334 HIS 0.009 0.001 HIS Y 333 Details of bonding type rmsd covalent geometry : bond 0.00367 (31008) covalent geometry : angle 0.65895 (41992) SS BOND : bond 0.00323 ( 106) SS BOND : angle 1.23015 ( 212) hydrogen bonds : bond 0.03742 ( 1004) hydrogen bonds : angle 5.91544 ( 2778) link_NAG-ASN : bond 0.00304 ( 24) link_NAG-ASN : angle 2.03597 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 TYR cc_start: 0.7119 (m-80) cc_final: 0.6648 (m-10) REVERT: C 305 MET cc_start: 0.7802 (mmm) cc_final: 0.7287 (mmt) REVERT: C 331 MET cc_start: 0.8902 (mpp) cc_final: 0.8438 (mpp) REVERT: E 511 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7466 (mt-10) REVERT: D 300 MET cc_start: 0.6476 (mmp) cc_final: 0.6182 (mmm) REVERT: D 352 ILE cc_start: 0.8447 (mm) cc_final: 0.8164 (pt) REVERT: F 480 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6321 (tp30) REVERT: Y 511 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7505 (mt-10) REVERT: X 103 LEU cc_start: 0.8099 (mm) cc_final: 0.7866 (mm) REVERT: X 107 GLN cc_start: 0.7516 (mt0) cc_final: 0.7142 (pp30) REVERT: X 305 MET cc_start: 0.7426 (ttt) cc_final: 0.6955 (ttm) REVERT: Z 85 TRP cc_start: 0.5876 (m-90) cc_final: 0.5485 (m100) outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.1770 time to fit residues: 36.3746 Evaluate side-chains 91 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 314 optimal weight: 0.5980 chunk 367 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 337 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN E 443 HIS D 62 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 330 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 187 GLN ** Z 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.051861 restraints weight = 315290.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.053044 restraints weight = 188550.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.053900 restraints weight = 128457.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.054466 restraints weight = 96720.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.054845 restraints weight = 78461.612| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 1.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31138 Z= 0.105 Angle : 0.573 13.055 42276 Z= 0.288 Chirality : 0.042 0.205 4648 Planarity : 0.004 0.051 5500 Dihedral : 5.182 41.181 4756 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.06 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3720 helix: 0.43 (0.17), residues: 924 sheet: -1.12 (0.17), residues: 952 loop : -1.76 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 171 TYR 0.019 0.001 TYR D 279 PHE 0.011 0.001 PHE F 433 TRP 0.025 0.001 TRP F 85 HIS 0.006 0.001 HIS F 114 Details of bonding type rmsd covalent geometry : bond 0.00228 (31008) covalent geometry : angle 0.56616 (41992) SS BOND : bond 0.00204 ( 106) SS BOND : angle 1.00749 ( 212) hydrogen bonds : bond 0.03178 ( 1004) hydrogen bonds : angle 5.39254 ( 2778) link_NAG-ASN : bond 0.00258 ( 24) link_NAG-ASN : angle 1.64185 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.37 seconds wall clock time: 97 minutes 19.08 seconds (5839.08 seconds total)