Starting phenix.real_space_refine on Thu Sep 26 22:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/09_2024/6pm6_20389.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.060 sd= 3.254 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9185 2.51 5 N 2260 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14100 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 8.70, per 1000 atoms: 0.62 Number of scatterers: 14100 At special positions: 0 Unit cell: (106.167, 102.875, 134.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2555 8.00 N 2260 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 38.6% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.523A pdb=" N PHE A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.972A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.522A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.951A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.518A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 286 removed outlier: 3.575A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.550A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.577A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 4.010A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.541A pdb=" N PHE D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.014A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.556A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.024A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.800A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.550A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 286 removed outlier: 3.558A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 283 " --> pdb=" O MET D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 304 through 325 removed outlier: 3.551A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 406 removed outlier: 4.396A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 427 removed outlier: 4.009A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.544A pdb=" N PHE B 29 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.904A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.056A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.530A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 286 removed outlier: 3.544A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 304 through 325 removed outlier: 3.637A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.552A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 427 removed outlier: 4.020A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.577A pdb=" N PHE C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.980A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.503A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.537A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 286 removed outlier: 3.538A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 304 through 325 removed outlier: 3.575A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.561A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 427 removed outlier: 3.942A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.567A pdb=" N PHE E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.964A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.531A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.980A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.538A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 286 removed outlier: 4.224A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 283 " --> pdb=" O MET E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 304 through 325 removed outlier: 3.567A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 406 removed outlier: 3.554A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 427 removed outlier: 3.964A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.556A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.630A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.555A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.582A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.587A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 677 hydrogen bonds defined for protein. 1968 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: 4.70 Time building geometry restraints manager: 3.92 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: 4313 1.34 - 1.47: 3630 1.47 - 1.59: 6332 1.59 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14445 Sorted by residual: bond pdb=" C PHE D 410 " pdb=" N PRO D 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C PHE A 410 " pdb=" N PRO A 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.70e+01 bond pdb=" C PHE E 410 " pdb=" N PRO E 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.69e+01 bond pdb=" C PHE C 410 " pdb=" N PRO C 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C PHE B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.61e+01 ... (remaining 14440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 18878 2.07 - 4.14: 582 4.14 - 6.21: 96 6.21 - 8.28: 45 8.28 - 10.35: 9 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8347 16.01 - 32.02: 339 32.02 - 48.03: 51 48.03 - 64.05: 45 64.05 - 80.06: 33 Dihedral angle restraints: 8815 sinusoidal: 3700 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 51.08 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 51.12 41.88 1 1.00e+01 1.00e-02 2.45e+01 ... (remaining 8812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1553 0.051 - 0.101: 538 0.101 - 0.152: 139 0.152 - 0.202: 15 0.202 - 0.253: 15 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.03e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO B 411 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.16e+00 pdb=" N PRO D 411 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO A 411 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.042 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4537 2.85 - 3.36: 12059 3.36 - 3.87: 22417 3.87 - 4.39: 26556 4.39 - 4.90: 44747 Nonbonded interactions: 110316 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.336 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.344 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.346 3.040 ... (remaining 110311 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 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.940 Find NCS groups from input model: 0.810 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14445 Z= 0.299 Angle : 0.922 10.349 19610 Z= 0.481 Chirality : 0.055 0.253 2260 Planarity : 0.007 0.076 2430 Dihedral : 11.654 80.057 5465 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.15), residues: 1710 helix: -4.79 (0.07), residues: 550 sheet: -1.89 (0.23), residues: 385 loop : -2.57 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 110 HIS 0.002 0.001 HIS C 125 PHE 0.021 0.002 PHE A 115 TYR 0.017 0.002 TYR D 425 ARG 0.008 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.635 Fit side-chains REVERT: A 75 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6919 (ttm110) REVERT: A 206 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8047 (mttt) REVERT: A 210 ASP cc_start: 0.8048 (m-30) cc_final: 0.7306 (t0) REVERT: A 222 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7579 (pttt) REVERT: A 292 LYS cc_start: 0.8062 (mttt) cc_final: 0.7690 (mttp) REVERT: A 391 MET cc_start: 0.6841 (mtp) cc_final: 0.6363 (tmm) REVERT: A 419 ILE cc_start: 0.8385 (mt) cc_final: 0.8131 (mp) REVERT: D 32 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7965 (tmtt) REVERT: D 75 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7024 (ttm110) REVERT: D 206 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8012 (mtmm) REVERT: D 210 ASP cc_start: 0.7951 (m-30) cc_final: 0.7046 (t0) REVERT: D 222 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7490 (pttt) REVERT: D 292 LYS cc_start: 0.8120 (mttt) cc_final: 0.7861 (mttp) REVERT: D 391 MET cc_start: 0.6743 (mtp) cc_final: 0.5594 (tpt) REVERT: D 420 PHE cc_start: 0.7334 (t80) cc_final: 0.7096 (t80) REVERT: B 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8034 (tmtt) REVERT: B 210 ASP cc_start: 0.7886 (m-30) cc_final: 0.7079 (t0) REVERT: B 222 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7573 (pttt) REVERT: B 279 MET cc_start: 0.8169 (mmm) cc_final: 0.7597 (mmt) REVERT: B 292 LYS cc_start: 0.8105 (mttt) cc_final: 0.7756 (mttp) REVERT: B 401 ARG cc_start: 0.5233 (tpt170) cc_final: 0.4987 (tmt90) REVERT: C 28 GLU cc_start: 0.7625 (tp30) cc_final: 0.7023 (tp30) REVERT: C 32 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8095 (tttp) REVERT: C 75 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7149 (mtp-110) REVERT: C 206 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7896 (mtmm) REVERT: C 210 ASP cc_start: 0.7846 (m-30) cc_final: 0.7070 (t0) REVERT: C 222 LYS cc_start: 0.7777 (ptmm) cc_final: 0.7488 (pttt) REVERT: C 420 PHE cc_start: 0.7290 (t80) cc_final: 0.7039 (t80) REVERT: E 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8044 (tmtt) REVERT: E 75 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7128 (ttm110) REVERT: E 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8100 (mtmm) REVERT: E 210 ASP cc_start: 0.7856 (m-30) cc_final: 0.7050 (t0) REVERT: E 391 MET cc_start: 0.6643 (mtp) cc_final: 0.6382 (ttp) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.9785 time to fit residues: 437.7165 Evaluate side-chains 285 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 77 ASN D 219 ASN D 231 HIS B 77 ASN B 231 HIS C 77 ASN C 219 ASN C 231 HIS E 77 ASN E 219 ASN E 231 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14445 Z= 0.214 Angle : 0.775 14.514 19610 Z= 0.394 Chirality : 0.050 0.336 2260 Planarity : 0.005 0.051 2430 Dihedral : 10.066 59.757 2185 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.77 % Allowed : 10.96 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.17), residues: 1710 helix: -3.05 (0.16), residues: 565 sheet: -1.06 (0.26), residues: 385 loop : -2.39 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 84 HIS 0.004 0.001 HIS B 231 PHE 0.013 0.001 PHE E 414 TYR 0.018 0.002 TYR B 317 ARG 0.007 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 313 time to evaluate : 1.535 Fit side-chains REVERT: A 75 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6987 (ttm110) REVERT: A 96 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7386 (t0) REVERT: A 179 MET cc_start: 0.8494 (mmm) cc_final: 0.7978 (tpt) REVERT: A 206 LYS cc_start: 0.8303 (mtpt) cc_final: 0.8064 (mttt) REVERT: A 212 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7329 (ptp-110) REVERT: A 292 LYS cc_start: 0.8118 (mttt) cc_final: 0.7756 (mttp) REVERT: A 303 MET cc_start: 0.8812 (mmm) cc_final: 0.8545 (mmt) REVERT: A 391 MET cc_start: 0.6674 (mtp) cc_final: 0.6426 (tmm) REVERT: A 420 PHE cc_start: 0.7677 (t80) cc_final: 0.6898 (t80) REVERT: D 62 ASN cc_start: 0.8495 (m-40) cc_final: 0.8282 (t0) REVERT: D 75 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7056 (ttm110) REVERT: D 138 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8469 (mttm) REVERT: D 179 MET cc_start: 0.8439 (tpt) cc_final: 0.7957 (tpt) REVERT: D 229 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8017 (mmm-85) REVERT: D 243 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6129 (mpt) REVERT: D 292 LYS cc_start: 0.8111 (mttt) cc_final: 0.7848 (mttp) REVERT: D 391 MET cc_start: 0.6723 (mtp) cc_final: 0.6495 (ttp) REVERT: B 97 ASP cc_start: 0.7704 (m-30) cc_final: 0.7427 (t0) REVERT: B 210 ASP cc_start: 0.7775 (m-30) cc_final: 0.7144 (t0) REVERT: B 222 LYS cc_start: 0.7948 (ptmm) cc_final: 0.7529 (pttt) REVERT: B 243 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.5843 (mpt) REVERT: B 292 LYS cc_start: 0.8084 (mttt) cc_final: 0.7762 (mttp) REVERT: B 420 PHE cc_start: 0.7653 (t80) cc_final: 0.7099 (t80) REVERT: C 75 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7175 (mtp-110) REVERT: C 96 ASP cc_start: 0.8000 (t0) cc_final: 0.7688 (t0) REVERT: C 97 ASP cc_start: 0.7647 (m-30) cc_final: 0.7278 (t0) REVERT: C 206 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7839 (mtmm) REVERT: C 243 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.5877 (mpt) REVERT: C 401 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5265 (tmt90) REVERT: C 420 PHE cc_start: 0.7356 (t80) cc_final: 0.7113 (t80) REVERT: E 34 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6891 (tpp) REVERT: E 75 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7176 (ttm110) REVERT: E 96 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7382 (t0) REVERT: E 97 ASP cc_start: 0.7930 (m-30) cc_final: 0.7642 (t0) REVERT: E 206 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8100 (mmmm) REVERT: E 210 ASP cc_start: 0.7874 (m-30) cc_final: 0.7172 (t0) REVERT: E 212 ARG cc_start: 0.7286 (ptp-110) cc_final: 0.6964 (ptp-110) REVERT: E 243 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.5944 (mpt) REVERT: E 262 MET cc_start: 0.4235 (mpp) cc_final: 0.3798 (mpp) REVERT: E 391 MET cc_start: 0.6796 (mtp) cc_final: 0.6562 (ttp) outliers start: 42 outliers final: 14 residues processed: 338 average time/residue: 1.0609 time to fit residues: 397.6296 Evaluate side-chains 291 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 267 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 0.0970 chunk 167 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 141 ASN D 82 GLN D 85 ASN D 141 ASN D 219 ASN B 82 GLN B 219 ASN C 82 GLN C 219 ASN E 82 GLN E 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14445 Z= 0.189 Angle : 0.707 12.500 19610 Z= 0.357 Chirality : 0.047 0.242 2260 Planarity : 0.004 0.047 2430 Dihedral : 8.249 57.680 2185 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.96 % Allowed : 14.79 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.18), residues: 1710 helix: -2.22 (0.18), residues: 570 sheet: -0.27 (0.28), residues: 340 loop : -2.24 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 255 HIS 0.001 0.000 HIS B 125 PHE 0.010 0.001 PHE E 414 TYR 0.014 0.002 TYR E 317 ARG 0.007 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 296 time to evaluate : 1.602 Fit side-chains REVERT: A 75 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7122 (ttm110) REVERT: A 179 MET cc_start: 0.8528 (mmm) cc_final: 0.8163 (tpt) REVERT: A 212 ARG cc_start: 0.7513 (ptp-110) cc_final: 0.7252 (ptp-110) REVERT: A 227 GLU cc_start: 0.8141 (pt0) cc_final: 0.7892 (pt0) REVERT: A 292 LYS cc_start: 0.8133 (mttt) cc_final: 0.7773 (mttp) REVERT: A 418 ASN cc_start: 0.7399 (m-40) cc_final: 0.7190 (m110) REVERT: A 420 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6952 (t80) REVERT: D 62 ASN cc_start: 0.8490 (t0) cc_final: 0.8275 (t0) REVERT: D 75 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7160 (ttm110) REVERT: D 97 ASP cc_start: 0.7657 (m-30) cc_final: 0.7411 (t0) REVERT: D 138 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8460 (mttm) REVERT: D 210 ASP cc_start: 0.7858 (m-30) cc_final: 0.7481 (m-30) REVERT: D 229 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7876 (mmt90) REVERT: D 292 LYS cc_start: 0.8171 (mttt) cc_final: 0.7922 (mttp) REVERT: B 72 MET cc_start: 0.8832 (mtt) cc_final: 0.8595 (mtt) REVERT: B 96 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7497 (t0) REVERT: B 138 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8339 (mttp) REVERT: B 210 ASP cc_start: 0.7748 (m-30) cc_final: 0.7440 (m-30) REVERT: C 75 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7112 (ttm110) REVERT: C 96 ASP cc_start: 0.8026 (t0) cc_final: 0.7791 (t0) REVERT: C 97 ASP cc_start: 0.7677 (m-30) cc_final: 0.7313 (t0) REVERT: C 243 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.5842 (mpt) REVERT: C 391 MET cc_start: 0.5017 (tmm) cc_final: 0.4506 (tmm) REVERT: C 401 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5345 (tmt90) REVERT: E 75 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7231 (ttm110) REVERT: E 96 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7551 (t0) REVERT: E 130 ASP cc_start: 0.7864 (m-30) cc_final: 0.7632 (t0) REVERT: E 206 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8102 (mmmm) REVERT: E 210 ASP cc_start: 0.7846 (m-30) cc_final: 0.7532 (m-30) REVERT: E 262 MET cc_start: 0.4617 (mpp) cc_final: 0.4239 (mpp) REVERT: E 418 ASN cc_start: 0.7417 (t0) cc_final: 0.7074 (m110) outliers start: 60 outliers final: 14 residues processed: 329 average time/residue: 0.9416 time to fit residues: 349.9015 Evaluate side-chains 296 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 274 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 282 GLN D 219 ASN B 219 ASN C 219 ASN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14445 Z= 0.192 Angle : 0.662 9.488 19610 Z= 0.337 Chirality : 0.046 0.184 2260 Planarity : 0.004 0.046 2430 Dihedral : 6.468 49.559 2185 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.36 % Allowed : 16.83 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.19), residues: 1710 helix: -1.68 (0.20), residues: 575 sheet: 0.07 (0.29), residues: 340 loop : -2.10 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 255 HIS 0.001 0.000 HIS C 125 PHE 0.011 0.001 PHE D 414 TYR 0.013 0.002 TYR B 317 ARG 0.009 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 283 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8710 (mttt) cc_final: 0.8214 (mtpt) REVERT: A 75 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7193 (ttm110) REVERT: A 163 MET cc_start: 0.8264 (mtm) cc_final: 0.8006 (mpp) REVERT: A 260 ILE cc_start: 0.4944 (OUTLIER) cc_final: 0.4730 (pt) REVERT: A 292 LYS cc_start: 0.8174 (mttt) cc_final: 0.7848 (mttp) REVERT: A 401 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5046 (tmt90) REVERT: D 75 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7191 (ttm110) REVERT: D 210 ASP cc_start: 0.7815 (m-30) cc_final: 0.7524 (m-30) REVERT: D 292 LYS cc_start: 0.8228 (mttt) cc_final: 0.7977 (mttp) REVERT: D 303 MET cc_start: 0.9047 (mmt) cc_final: 0.8733 (mmt) REVERT: D 420 PHE cc_start: 0.7255 (t80) cc_final: 0.7022 (t80) REVERT: B 72 MET cc_start: 0.8837 (mtt) cc_final: 0.8595 (mtt) REVERT: B 96 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 108 SER cc_start: 0.8802 (t) cc_final: 0.8591 (m) REVERT: B 210 ASP cc_start: 0.7777 (m-30) cc_final: 0.7491 (m-30) REVERT: C 49 LYS cc_start: 0.8714 (mttt) cc_final: 0.8164 (mmtm) REVERT: C 75 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7140 (ttm110) REVERT: C 156 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7097 (mmt) REVERT: C 243 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.5769 (mpt) REVERT: C 391 MET cc_start: 0.4719 (tmm) cc_final: 0.4287 (tmm) REVERT: C 401 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5445 (tmt90) REVERT: C 420 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6932 (t80) REVERT: E 75 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7259 (ttm110) REVERT: E 97 ASP cc_start: 0.7930 (m-30) cc_final: 0.7669 (t0) REVERT: E 108 SER cc_start: 0.8918 (t) cc_final: 0.8639 (t) REVERT: E 120 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: E 130 ASP cc_start: 0.7880 (m-30) cc_final: 0.7662 (t0) REVERT: E 156 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6964 (mmt) REVERT: E 210 ASP cc_start: 0.7834 (m-30) cc_final: 0.7481 (m-30) REVERT: E 227 GLU cc_start: 0.8209 (pt0) cc_final: 0.7985 (pt0) REVERT: E 229 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7764 (mmm-85) REVERT: E 262 MET cc_start: 0.4855 (mpp) cc_final: 0.4371 (mpp) outliers start: 66 outliers final: 16 residues processed: 314 average time/residue: 0.9867 time to fit residues: 346.6570 Evaluate side-chains 295 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 229 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 122 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 219 ASN D 219 ASN B 219 ASN C 62 ASN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14445 Z= 0.200 Angle : 0.657 12.404 19610 Z= 0.334 Chirality : 0.045 0.157 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.824 40.241 2185 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.36 % Allowed : 17.03 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1710 helix: -1.32 (0.20), residues: 575 sheet: 0.22 (0.29), residues: 340 loop : -1.97 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 255 HIS 0.001 0.001 HIS C 125 PHE 0.014 0.001 PHE D 414 TYR 0.014 0.002 TYR A 144 ARG 0.006 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 281 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8722 (mttt) cc_final: 0.8228 (mtpt) REVERT: A 75 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7180 (ttm110) REVERT: A 225 CYS cc_start: 0.6047 (t) cc_final: 0.5813 (t) REVERT: A 227 GLU cc_start: 0.8255 (pt0) cc_final: 0.7924 (pt0) REVERT: A 243 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5788 (mpt) REVERT: A 292 LYS cc_start: 0.8207 (mttt) cc_final: 0.7873 (mttp) REVERT: A 420 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: D 75 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7178 (ttm110) REVERT: D 97 ASP cc_start: 0.7616 (m-30) cc_final: 0.7413 (t0) REVERT: D 130 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7516 (t0) REVERT: D 138 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8487 (mttm) REVERT: D 210 ASP cc_start: 0.7811 (m-30) cc_final: 0.7468 (m-30) REVERT: D 243 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.5984 (mpt) REVERT: D 292 LYS cc_start: 0.8254 (mttt) cc_final: 0.8000 (mttp) REVERT: D 303 MET cc_start: 0.9054 (mmt) cc_final: 0.8755 (mmt) REVERT: D 420 PHE cc_start: 0.7255 (t80) cc_final: 0.7023 (t80) REVERT: B 72 MET cc_start: 0.8828 (mtt) cc_final: 0.8556 (mtt) REVERT: B 210 ASP cc_start: 0.7751 (m-30) cc_final: 0.7470 (m-30) REVERT: B 227 GLU cc_start: 0.8174 (pt0) cc_final: 0.7937 (pt0) REVERT: B 418 ASN cc_start: 0.7443 (m-40) cc_final: 0.7228 (m110) REVERT: C 49 LYS cc_start: 0.8670 (mttt) cc_final: 0.8113 (mmtm) REVERT: C 75 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7137 (ttm110) REVERT: C 210 ASP cc_start: 0.7867 (m-30) cc_final: 0.7517 (m-30) REVERT: C 212 ARG cc_start: 0.7451 (ptp-110) cc_final: 0.7099 (ptp-170) REVERT: C 243 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.5600 (mpt) REVERT: C 391 MET cc_start: 0.4688 (tmm) cc_final: 0.4242 (tmm) REVERT: C 401 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5541 (tmt90) REVERT: C 420 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6962 (t80) REVERT: E 75 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7262 (ttm110) REVERT: E 96 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7648 (t0) REVERT: E 108 SER cc_start: 0.8887 (t) cc_final: 0.8634 (t) REVERT: E 120 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8006 (ttmt) REVERT: E 130 ASP cc_start: 0.7869 (m-30) cc_final: 0.7657 (t0) REVERT: E 227 GLU cc_start: 0.8157 (pt0) cc_final: 0.7897 (pt0) REVERT: E 262 MET cc_start: 0.4839 (mpp) cc_final: 0.4368 (mpp) outliers start: 66 outliers final: 23 residues processed: 313 average time/residue: 0.9856 time to fit residues: 345.7043 Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 273 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN D 282 GLN B 219 ASN C 282 GLN E 219 ASN E 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14445 Z= 0.187 Angle : 0.639 9.039 19610 Z= 0.324 Chirality : 0.045 0.157 2260 Planarity : 0.004 0.042 2430 Dihedral : 5.358 46.967 2185 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.69 % Allowed : 17.43 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1710 helix: -0.94 (0.21), residues: 580 sheet: 0.25 (0.28), residues: 360 loop : -1.58 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 255 HIS 0.001 0.001 HIS C 231 PHE 0.013 0.001 PHE D 414 TYR 0.013 0.002 TYR A 144 ARG 0.008 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 289 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7178 (ttm110) REVERT: A 163 MET cc_start: 0.8232 (mtm) cc_final: 0.7928 (mpp) REVERT: A 227 GLU cc_start: 0.8246 (pt0) cc_final: 0.7925 (pt0) REVERT: A 292 LYS cc_start: 0.8227 (mttt) cc_final: 0.7889 (mttp) REVERT: A 401 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.4828 (tmt90) REVERT: A 420 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: D 75 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7204 (ttm110) REVERT: D 130 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7582 (t0) REVERT: D 210 ASP cc_start: 0.7798 (m-30) cc_final: 0.7394 (m-30) REVERT: D 243 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.5963 (mpt) REVERT: D 292 LYS cc_start: 0.8274 (mttt) cc_final: 0.8024 (mttp) REVERT: D 420 PHE cc_start: 0.7187 (t80) cc_final: 0.6928 (t80) REVERT: B 28 GLU cc_start: 0.7676 (tp30) cc_final: 0.7002 (tp30) REVERT: B 72 MET cc_start: 0.8828 (mtt) cc_final: 0.8557 (mtt) REVERT: B 210 ASP cc_start: 0.7779 (m-30) cc_final: 0.7508 (m-30) REVERT: B 227 GLU cc_start: 0.8173 (pt0) cc_final: 0.7816 (pt0) REVERT: C 49 LYS cc_start: 0.8678 (mttt) cc_final: 0.8209 (mmtt) REVERT: C 75 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7119 (ttm110) REVERT: C 97 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7407 (t0) REVERT: C 210 ASP cc_start: 0.7851 (m-30) cc_final: 0.7539 (m-30) REVERT: C 212 ARG cc_start: 0.7458 (ptp-110) cc_final: 0.7009 (ptp-170) REVERT: C 227 GLU cc_start: 0.8276 (pt0) cc_final: 0.8057 (pt0) REVERT: C 229 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7237 (mmt90) REVERT: C 243 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.5521 (mpt) REVERT: C 262 MET cc_start: 0.4262 (mpp) cc_final: 0.3990 (mpp) REVERT: C 391 MET cc_start: 0.4450 (tmm) cc_final: 0.4000 (tmm) REVERT: C 401 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5600 (tmt90) REVERT: E 49 LYS cc_start: 0.8713 (mttt) cc_final: 0.8284 (mmtt) REVERT: E 75 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7248 (ttm110) REVERT: E 108 SER cc_start: 0.8900 (t) cc_final: 0.8605 (t) REVERT: E 120 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8034 (ttmt) REVERT: E 130 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7652 (t0) REVERT: E 156 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.6727 (mmt) REVERT: E 227 GLU cc_start: 0.8134 (pt0) cc_final: 0.7863 (pt0) REVERT: E 262 MET cc_start: 0.4931 (mpp) cc_final: 0.4335 (mpp) outliers start: 71 outliers final: 28 residues processed: 322 average time/residue: 1.0111 time to fit residues: 362.8889 Evaluate side-chains 321 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 282 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN D 282 GLN B 219 ASN B 282 GLN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14445 Z= 0.182 Angle : 0.647 12.460 19610 Z= 0.328 Chirality : 0.044 0.176 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.327 45.692 2185 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.16 % Allowed : 19.01 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1710 helix: -0.64 (0.21), residues: 580 sheet: 0.26 (0.28), residues: 360 loop : -1.48 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 255 HIS 0.002 0.001 HIS A 231 PHE 0.016 0.001 PHE E 414 TYR 0.013 0.001 TYR A 144 ARG 0.007 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7169 (ttm110) REVERT: A 227 GLU cc_start: 0.8232 (pt0) cc_final: 0.7915 (pt0) REVERT: A 292 LYS cc_start: 0.8231 (mttt) cc_final: 0.7894 (mttp) REVERT: A 420 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: D 75 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7202 (ttm110) REVERT: D 108 SER cc_start: 0.8874 (t) cc_final: 0.8621 (t) REVERT: D 120 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (ttmp) REVERT: D 130 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7500 (t0) REVERT: D 135 ARG cc_start: 0.7785 (ptp-170) cc_final: 0.7566 (mtm-85) REVERT: D 210 ASP cc_start: 0.7779 (m-30) cc_final: 0.7363 (m-30) REVERT: D 212 ARG cc_start: 0.7306 (ptp-110) cc_final: 0.7057 (ptp-170) REVERT: D 225 CYS cc_start: 0.5921 (t) cc_final: 0.5631 (t) REVERT: D 243 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.5890 (mpt) REVERT: D 420 PHE cc_start: 0.7174 (t80) cc_final: 0.6918 (t80) REVERT: B 28 GLU cc_start: 0.7714 (tp30) cc_final: 0.7020 (tp30) REVERT: B 130 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (t0) REVERT: B 210 ASP cc_start: 0.7778 (m-30) cc_final: 0.7516 (m-30) REVERT: B 227 GLU cc_start: 0.8197 (pt0) cc_final: 0.7901 (pt0) REVERT: B 229 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8174 (mmm-85) REVERT: B 243 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.5841 (mpt) REVERT: C 49 LYS cc_start: 0.8690 (mttt) cc_final: 0.8222 (mmtt) REVERT: C 75 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7123 (ttm110) REVERT: C 210 ASP cc_start: 0.7854 (m-30) cc_final: 0.7517 (m-30) REVERT: C 212 ARG cc_start: 0.7435 (ptp-110) cc_final: 0.7158 (ptp-170) REVERT: C 227 GLU cc_start: 0.8213 (pt0) cc_final: 0.7982 (pt0) REVERT: C 243 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.5395 (mpt) REVERT: C 391 MET cc_start: 0.4245 (tmm) cc_final: 0.3823 (tmm) REVERT: C 401 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5565 (tmt90) REVERT: E 49 LYS cc_start: 0.8653 (mttt) cc_final: 0.8230 (mmtt) REVERT: E 75 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7245 (ttm110) REVERT: E 108 SER cc_start: 0.8904 (t) cc_final: 0.8603 (t) REVERT: E 120 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: E 156 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.6690 (mmt) REVERT: E 262 MET cc_start: 0.4931 (mpp) cc_final: 0.4385 (mpp) outliers start: 63 outliers final: 30 residues processed: 316 average time/residue: 1.0566 time to fit residues: 371.6497 Evaluate side-chains 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 276 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 418 ASN D 219 ASN D 282 GLN B 219 ASN B 282 GLN B 418 ASN E 219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14445 Z= 0.167 Angle : 0.634 9.571 19610 Z= 0.320 Chirality : 0.044 0.159 2260 Planarity : 0.004 0.043 2430 Dihedral : 5.191 48.329 2185 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.03 % Allowed : 19.67 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1710 helix: -0.32 (0.22), residues: 580 sheet: 0.29 (0.28), residues: 360 loop : -1.40 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 255 HIS 0.002 0.001 HIS A 231 PHE 0.011 0.001 PHE D 414 TYR 0.011 0.001 TYR E 144 ARG 0.008 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 285 time to evaluate : 1.397 Fit side-chains REVERT: A 75 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7177 (ttm110) REVERT: A 108 SER cc_start: 0.8913 (t) cc_final: 0.8652 (t) REVERT: A 227 GLU cc_start: 0.8242 (pt0) cc_final: 0.7911 (pt0) REVERT: A 292 LYS cc_start: 0.8223 (mttt) cc_final: 0.7884 (mttp) REVERT: A 420 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: D 75 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7218 (ttm110) REVERT: D 108 SER cc_start: 0.8886 (t) cc_final: 0.8632 (t) REVERT: D 130 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7498 (t0) REVERT: D 212 ARG cc_start: 0.7270 (ptp-110) cc_final: 0.7057 (ptp-170) REVERT: D 225 CYS cc_start: 0.6129 (t) cc_final: 0.5845 (t) REVERT: D 243 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.5934 (mpt) REVERT: D 420 PHE cc_start: 0.7188 (t80) cc_final: 0.6932 (t80) REVERT: B 28 GLU cc_start: 0.7704 (tp30) cc_final: 0.7026 (tp30) REVERT: B 34 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6744 (tpp) REVERT: B 130 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7565 (t0) REVERT: B 210 ASP cc_start: 0.7749 (m-30) cc_final: 0.7488 (m-30) REVERT: B 229 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8224 (mmm-85) REVERT: C 49 LYS cc_start: 0.8675 (mttt) cc_final: 0.8230 (mmtt) REVERT: C 75 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7131 (ttm110) REVERT: C 210 ASP cc_start: 0.7851 (m-30) cc_final: 0.7523 (m-30) REVERT: C 212 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.7112 (ptp-170) REVERT: C 227 GLU cc_start: 0.8163 (pt0) cc_final: 0.7959 (pt0) REVERT: C 243 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.5331 (mpt) REVERT: E 49 LYS cc_start: 0.8663 (mttt) cc_final: 0.8252 (mmtt) REVERT: E 75 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7253 (ttm110) REVERT: E 96 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7880 (t0) REVERT: E 108 SER cc_start: 0.8905 (t) cc_final: 0.8629 (t) REVERT: E 156 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6659 (mmt) REVERT: E 262 MET cc_start: 0.4907 (mpp) cc_final: 0.4368 (mpp) outliers start: 61 outliers final: 25 residues processed: 309 average time/residue: 0.9880 time to fit residues: 340.6900 Evaluate side-chains 305 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0870 chunk 143 optimal weight: 0.0570 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 418 ASN D 171 GLN D 180 ASN D 219 ASN B 219 ASN B 282 GLN B 418 ASN E 219 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14445 Z= 0.183 Angle : 0.661 12.738 19610 Z= 0.333 Chirality : 0.044 0.160 2260 Planarity : 0.004 0.036 2430 Dihedral : 5.281 46.374 2185 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.30 % Allowed : 20.46 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1710 helix: -0.05 (0.22), residues: 580 sheet: 0.34 (0.28), residues: 365 loop : -1.41 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 255 HIS 0.002 0.001 HIS E 217 PHE 0.011 0.001 PHE E 414 TYR 0.012 0.001 TYR E 144 ARG 0.008 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 279 time to evaluate : 1.469 Fit side-chains REVERT: A 75 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7174 (ttm110) REVERT: A 108 SER cc_start: 0.8925 (t) cc_final: 0.8660 (t) REVERT: A 227 GLU cc_start: 0.8225 (pt0) cc_final: 0.7879 (pt0) REVERT: A 292 LYS cc_start: 0.8240 (mttt) cc_final: 0.7900 (mttp) REVERT: A 420 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: D 75 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7217 (ttm110) REVERT: D 108 SER cc_start: 0.8899 (t) cc_final: 0.8624 (t) REVERT: D 130 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (t0) REVERT: D 212 ARG cc_start: 0.7381 (ptp-110) cc_final: 0.7131 (ptp-170) REVERT: D 243 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.5935 (mpt) REVERT: D 420 PHE cc_start: 0.7196 (t80) cc_final: 0.6934 (t80) REVERT: B 28 GLU cc_start: 0.7713 (tp30) cc_final: 0.7043 (tp30) REVERT: B 34 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6702 (tpp) REVERT: B 130 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7582 (t0) REVERT: B 179 MET cc_start: 0.8292 (tpt) cc_final: 0.7936 (tpt) REVERT: B 210 ASP cc_start: 0.7736 (m-30) cc_final: 0.7493 (m-30) REVERT: B 420 PHE cc_start: 0.7758 (m-80) cc_final: 0.7427 (t80) REVERT: C 49 LYS cc_start: 0.8668 (mttt) cc_final: 0.8225 (mmtt) REVERT: C 75 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7134 (ttm110) REVERT: C 210 ASP cc_start: 0.7847 (m-30) cc_final: 0.7525 (m-30) REVERT: C 212 ARG cc_start: 0.7416 (ptp-110) cc_final: 0.7108 (ptp-170) REVERT: C 243 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5331 (mpt) REVERT: E 49 LYS cc_start: 0.8656 (mttt) cc_final: 0.8246 (mmtt) REVERT: E 75 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7254 (ttm110) REVERT: E 108 SER cc_start: 0.8916 (t) cc_final: 0.8634 (t) REVERT: E 156 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.6655 (mmt) REVERT: E 262 MET cc_start: 0.4819 (mpp) cc_final: 0.4301 (mpp) outliers start: 50 outliers final: 27 residues processed: 296 average time/residue: 0.9350 time to fit residues: 310.4330 Evaluate side-chains 304 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 270 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0000 chunk 76 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN B 219 ASN E 171 GLN E 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14445 Z= 0.185 Angle : 0.658 10.125 19610 Z= 0.331 Chirality : 0.044 0.159 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.307 48.858 2185 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.97 % Allowed : 21.32 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1710 helix: 0.16 (0.22), residues: 580 sheet: 0.27 (0.27), residues: 370 loop : -1.42 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 255 HIS 0.002 0.000 HIS A 231 PHE 0.011 0.001 PHE A 115 TYR 0.015 0.001 TYR A 144 ARG 0.008 0.000 ARG D 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 1.510 Fit side-chains REVERT: A 75 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7139 (ttm110) REVERT: A 108 SER cc_start: 0.8941 (t) cc_final: 0.8667 (t) REVERT: A 227 GLU cc_start: 0.8219 (pt0) cc_final: 0.7865 (pt0) REVERT: A 292 LYS cc_start: 0.8260 (mttt) cc_final: 0.7915 (mttp) REVERT: A 420 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: D 75 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7206 (ttm110) REVERT: D 108 SER cc_start: 0.8885 (t) cc_final: 0.8613 (t) REVERT: D 130 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7456 (t0) REVERT: D 212 ARG cc_start: 0.7336 (ptp-110) cc_final: 0.7093 (ptp-170) REVERT: D 420 PHE cc_start: 0.7223 (t80) cc_final: 0.6954 (t80) REVERT: B 28 GLU cc_start: 0.7721 (tp30) cc_final: 0.7052 (tp30) REVERT: B 34 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6688 (tpp) REVERT: B 130 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7601 (t0) REVERT: C 49 LYS cc_start: 0.8658 (mttt) cc_final: 0.8219 (mmtt) REVERT: C 75 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7122 (ttm110) REVERT: C 97 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7330 (t0) REVERT: C 210 ASP cc_start: 0.7857 (m-30) cc_final: 0.7528 (m-30) REVERT: C 212 ARG cc_start: 0.7451 (ptp-110) cc_final: 0.7116 (ptp-170) REVERT: C 243 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5280 (mpt) REVERT: C 420 PHE cc_start: 0.7594 (t80) cc_final: 0.6847 (t80) REVERT: E 49 LYS cc_start: 0.8630 (mttt) cc_final: 0.8218 (mmtt) REVERT: E 75 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7252 (ttm110) REVERT: E 108 SER cc_start: 0.8921 (t) cc_final: 0.8636 (t) REVERT: E 156 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6614 (mmt) REVERT: E 262 MET cc_start: 0.4814 (mpp) cc_final: 0.4327 (mpp) outliers start: 45 outliers final: 29 residues processed: 286 average time/residue: 0.9497 time to fit residues: 304.9767 Evaluate side-chains 301 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 265 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN B 219 ASN E 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126277 restraints weight = 15284.265| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.20 r_work: 0.3172 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14445 Z= 0.222 Angle : 0.684 11.747 19610 Z= 0.342 Chirality : 0.045 0.157 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.356 47.239 2185 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.84 % Allowed : 21.98 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1710 helix: 0.27 (0.22), residues: 580 sheet: 0.23 (0.27), residues: 370 loop : -1.40 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 PHE 0.013 0.001 PHE A 115 TYR 0.013 0.002 TYR A 317 ARG 0.008 0.001 ARG D 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5619.08 seconds wall clock time: 98 minutes 51.87 seconds (5931.87 seconds total)