Starting phenix.real_space_refine on Mon Mar 18 01:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwi_29505/03_2024/8fwi_29505_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwi_29505/03_2024/8fwi_29505.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/8fwi_29505/03_2024/8fwi_29505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwi_29505/03_2024/8fwi_29505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwi_29505/03_2024/8fwi_29505_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwi_29505/03_2024/8fwi_29505_trim_updated.pdb" } 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 34760 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 192 5.16 5 C 32220 2.51 5 N 9396 2.21 5 O 9972 1.98 5 H 51060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 434": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 434": "OE1" <-> "OE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 434": "OE1" <-> "OE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 102924 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "B" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "C" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "D" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "E" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "F" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "G" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "H" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "I" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "J" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "K" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "L" Number of atoms: 8511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8511 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 532} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 32.15, per 1000 atoms: 0.31 Number of scatterers: 102924 At special positions: 0 Unit cell: (115, 121, 315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 192 16.00 P 60 15.00 Mg 24 11.99 O 9972 8.00 N 9396 7.00 C 32220 6.00 H 51060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.20 Conformation dependent library (CDL) restraints added in 8.2 seconds 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11928 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 204 helices and 36 sheets defined 50.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 96 through 102 removed outlier: 3.777A pdb=" N ALA A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.754A pdb=" N VAL A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.766A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.638A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.882A pdb=" N TRP A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 removed outlier: 3.795A pdb=" N ALA B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.857A pdb=" N VAL B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.766A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 5.215A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 160 removed outlier: 3.537A pdb=" N ARG B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.636A pdb=" N SER B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.882A pdb=" N TRP B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP B 372 " --> pdb=" O THR B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 373 through 391 removed outlier: 3.724A pdb=" N ARG B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS B 478 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 removed outlier: 3.797A pdb=" N ALA C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.857A pdb=" N VAL C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.777A pdb=" N ALA C 101 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 5.217A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.756A pdb=" N VAL C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 removed outlier: 3.561A pdb=" N MET C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 293 removed outlier: 3.768A pdb=" N GLY C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.882A pdb=" N TRP C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY C 371 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 373 through 391 removed outlier: 3.724A pdb=" N ARG C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS C 478 " --> pdb=" O GLY C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.797A pdb=" N ALA D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.766A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.561A pdb=" N MET D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 293 removed outlier: 3.768A pdb=" N GLY D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 316 " --> pdb=" O MET D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.210A pdb=" N GLY D 371 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 372 " --> pdb=" O THR D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 372' Processing helix chain 'D' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS D 478 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 6.370A pdb=" N GLU E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.797A pdb=" N ALA E 41 " --> pdb=" O LYS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.777A pdb=" N ALA E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 160 removed outlier: 3.537A pdb=" N ARG E 159 " --> pdb=" O TRP E 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 293 removed outlier: 3.769A pdb=" N GLY E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 316 removed outlier: 3.636A pdb=" N SER E 314 " --> pdb=" O ARG E 310 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 315 " --> pdb=" O ASN E 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY E 316 " --> pdb=" O MET E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.880A pdb=" N TRP E 322 " --> pdb=" O ASP E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY E 371 " --> pdb=" O PHE E 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP E 372 " --> pdb=" O THR E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 372' Processing helix chain 'E' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS E 478 " --> pdb=" O GLY E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 18 removed outlier: 6.370A pdb=" N GLU F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 51 removed outlier: 3.795A pdb=" N ALA F 41 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 74 removed outlier: 3.857A pdb=" N VAL F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 96 through 102 removed outlier: 3.777A pdb=" N ALA F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 3.766A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU F 135 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG F 159 " --> pdb=" O TRP F 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 185 removed outlier: 3.756A pdb=" N VAL F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 293 removed outlier: 3.768A pdb=" N GLY F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER F 314 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 315 " --> pdb=" O ASN F 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 316 " --> pdb=" O MET F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP F 322 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY F 371 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP F 372 " --> pdb=" O THR F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 372' Processing helix chain 'F' and resid 373 through 391 removed outlier: 3.726A pdb=" N ARG F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS F 478 " --> pdb=" O GLY F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 16 " --> pdb=" O GLY G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL G 72 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 96 through 102 removed outlier: 3.778A pdb=" N ALA G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 123 removed outlier: 3.764A pdb=" N VAL G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 160 removed outlier: 3.537A pdb=" N ARG G 159 " --> pdb=" O TRP G 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 258 removed outlier: 3.561A pdb=" N MET G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY G 293 " --> pdb=" O ALA G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 316 removed outlier: 3.636A pdb=" N SER G 314 " --> pdb=" O ARG G 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU G 315 " --> pdb=" O ASN G 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP G 322 " --> pdb=" O ASP G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY G 371 " --> pdb=" O PHE G 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP G 372 " --> pdb=" O THR G 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 372' Processing helix chain 'G' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 553 removed outlier: 3.733A pdb=" N LYS G 478 " --> pdb=" O GLY G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 18 removed outlier: 6.370A pdb=" N GLU H 15 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA H 101 " --> pdb=" O PRO H 97 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU H 102 " --> pdb=" O SER H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG H 159 " --> pdb=" O TRP H 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 185 removed outlier: 3.754A pdb=" N VAL H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET H 256 " --> pdb=" O ASP H 252 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET H 257 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA H 258 " --> pdb=" O ASP H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY H 293 " --> pdb=" O ALA H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER H 314 " --> pdb=" O ARG H 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU H 315 " --> pdb=" O ASN H 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY H 316 " --> pdb=" O MET H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 326 removed outlier: 3.882A pdb=" N TRP H 322 " --> pdb=" O ASP H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 367 through 372 removed outlier: 4.210A pdb=" N GLY H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP H 372 " --> pdb=" O THR H 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 367 through 372' Processing helix chain 'H' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 553 removed outlier: 3.732A pdb=" N LYS H 478 " --> pdb=" O GLY H 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 18 removed outlier: 6.370A pdb=" N GLU I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU I 16 " --> pdb=" O GLY I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA I 41 " --> pdb=" O LYS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 74 removed outlier: 3.857A pdb=" N VAL I 72 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU I 102 " --> pdb=" O SER I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 removed outlier: 3.764A pdb=" N VAL I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 139 removed outlier: 5.215A pdb=" N LEU I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE I 139 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG I 159 " --> pdb=" O TRP I 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 185 removed outlier: 3.754A pdb=" N VAL I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP I 185 " --> pdb=" O GLU I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET I 256 " --> pdb=" O ASP I 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET I 257 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER I 314 " --> pdb=" O ARG I 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU I 315 " --> pdb=" O ASN I 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY I 316 " --> pdb=" O MET I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP I 322 " --> pdb=" O ASP I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 367 through 372 removed outlier: 4.210A pdb=" N GLY I 371 " --> pdb=" O PHE I 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP I 372 " --> pdb=" O THR I 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 367 through 372' Processing helix chain 'I' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 553 removed outlier: 3.734A pdb=" N LYS I 478 " --> pdb=" O GLY I 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 18 removed outlier: 6.372A pdb=" N GLU J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU J 16 " --> pdb=" O GLY J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL J 122 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 139 removed outlier: 5.216A pdb=" N LEU J 135 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA J 138 " --> pdb=" O SER J 134 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE J 139 " --> pdb=" O LEU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 160 removed outlier: 3.536A pdb=" N ARG J 159 " --> pdb=" O TRP J 155 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP J 185 " --> pdb=" O GLU J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET J 257 " --> pdb=" O LEU J 253 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 316 removed outlier: 3.638A pdb=" N SER J 314 " --> pdb=" O ARG J 310 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU J 315 " --> pdb=" O ASN J 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY J 316 " --> pdb=" O MET J 312 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 326 removed outlier: 3.882A pdb=" N TRP J 322 " --> pdb=" O ASP J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY J 371 " --> pdb=" O PHE J 367 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP J 372 " --> pdb=" O THR J 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 367 through 372' Processing helix chain 'J' and resid 373 through 391 removed outlier: 3.724A pdb=" N ARG J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY J 391 " --> pdb=" O LEU J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 553 removed outlier: 3.734A pdb=" N LYS J 478 " --> pdb=" O GLY J 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 18 removed outlier: 6.369A pdb=" N GLU K 15 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 86 Processing helix chain 'K' and resid 96 through 102 removed outlier: 3.777A pdb=" N ALA K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 123 removed outlier: 3.765A pdb=" N VAL K 122 " --> pdb=" O ALA K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 139 removed outlier: 5.215A pdb=" N LEU K 135 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA K 138 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE K 139 " --> pdb=" O LEU K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 160 removed outlier: 3.535A pdb=" N ARG K 159 " --> pdb=" O TRP K 155 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL K 183 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP K 185 " --> pdb=" O GLU K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 258 removed outlier: 3.561A pdb=" N MET K 256 " --> pdb=" O ASP K 252 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET K 257 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA K 258 " --> pdb=" O ASP K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 316 removed outlier: 3.638A pdb=" N SER K 314 " --> pdb=" O ARG K 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU K 315 " --> pdb=" O ASN K 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY K 316 " --> pdb=" O MET K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP K 322 " --> pdb=" O ASP K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY K 371 " --> pdb=" O PHE K 367 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP K 372 " --> pdb=" O THR K 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 367 through 372' Processing helix chain 'K' and resid 373 through 391 removed outlier: 3.725A pdb=" N ARG K 390 " --> pdb=" O PHE K 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY K 391 " --> pdb=" O LEU K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 553 removed outlier: 3.734A pdb=" N LYS K 478 " --> pdb=" O GLY K 474 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 18 removed outlier: 6.371A pdb=" N GLU L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 51 removed outlier: 3.796A pdb=" N ALA L 41 " --> pdb=" O LYS L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 74 removed outlier: 3.856A pdb=" N VAL L 72 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER L 74 " --> pdb=" O ASN L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 Processing helix chain 'L' and resid 96 through 102 removed outlier: 3.776A pdb=" N ALA L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU L 102 " --> pdb=" O SER L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 123 removed outlier: 3.766A pdb=" N VAL L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 139 removed outlier: 5.215A pdb=" N LEU L 135 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE L 139 " --> pdb=" O LEU L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 160 removed outlier: 3.537A pdb=" N ARG L 159 " --> pdb=" O TRP L 155 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 185 removed outlier: 3.755A pdb=" N VAL L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP L 185 " --> pdb=" O GLU L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 258 removed outlier: 3.560A pdb=" N MET L 256 " --> pdb=" O ASP L 252 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET L 257 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA L 258 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 293 removed outlier: 3.767A pdb=" N GLY L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 316 removed outlier: 3.637A pdb=" N SER L 314 " --> pdb=" O ARG L 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU L 315 " --> pdb=" O ASN L 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY L 316 " --> pdb=" O MET L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 326 removed outlier: 3.881A pdb=" N TRP L 322 " --> pdb=" O ASP L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 367 through 372 removed outlier: 4.211A pdb=" N GLY L 371 " --> pdb=" O PHE L 367 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP L 372 " --> pdb=" O THR L 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 367 through 372' Processing helix chain 'L' and resid 373 through 391 removed outlier: 3.726A pdb=" N ARG L 390 " --> pdb=" O PHE L 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 391 " --> pdb=" O LEU L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 553 removed outlier: 3.734A pdb=" N LYS L 478 " --> pdb=" O GLY L 474 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG A 25 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 163 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS A 186 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 32 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS A 192 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER A 199 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ILE A 222 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A 201 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE A 431 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET A 454 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 433 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU A 451 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 327 through 333 Processing sheet with id= 4, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG B 25 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 163 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS B 186 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER B 32 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS B 192 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER B 199 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE B 222 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B 201 " --> pdb=" O PHE B 220 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE B 431 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N MET B 454 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG B 433 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU B 451 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 327 through 333 Processing sheet with id= 7, first strand: chain 'C' and resid 87 through 93 removed outlier: 4.171A pdb=" N ARG C 25 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 163 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS C 186 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 32 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS C 192 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER C 199 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE C 222 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 201 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE C 431 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N MET C 454 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG C 433 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU C 451 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 327 through 333 Processing sheet with id= 10, first strand: chain 'D' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG D 25 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 163 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS D 186 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER D 32 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS D 192 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N SER D 199 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE D 222 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG D 201 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE D 431 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N MET D 454 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG D 433 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU D 451 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 327 through 333 Processing sheet with id= 13, first strand: chain 'E' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG E 25 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR E 163 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS E 186 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER E 32 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS E 192 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N SER E 199 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE E 222 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG E 201 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 267 through 272 removed outlier: 13.275A pdb=" N PHE E 431 " --> pdb=" O MET E 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET E 454 " --> pdb=" O PHE E 431 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG E 433 " --> pdb=" O PHE E 452 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU E 451 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 327 through 333 Processing sheet with id= 16, first strand: chain 'F' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG F 25 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR F 163 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS F 186 " --> pdb=" O PRO F 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER F 32 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS F 192 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N SER F 199 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ILE F 222 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG F 201 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE F 431 " --> pdb=" O MET F 454 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N MET F 454 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG F 433 " --> pdb=" O PHE F 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU F 451 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 327 through 333 Processing sheet with id= 19, first strand: chain 'G' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG G 25 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR G 163 " --> pdb=" O ARG G 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS G 186 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER G 32 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS G 192 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N SER G 199 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ILE G 222 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG G 201 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 267 through 272 removed outlier: 13.275A pdb=" N PHE G 431 " --> pdb=" O MET G 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET G 454 " --> pdb=" O PHE G 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG G 433 " --> pdb=" O PHE G 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU G 451 " --> pdb=" O LEU G 462 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 327 through 333 Processing sheet with id= 22, first strand: chain 'H' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG H 25 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR H 163 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS H 186 " --> pdb=" O PRO H 26 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER H 32 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS H 192 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER H 199 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE H 222 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG H 201 " --> pdb=" O PHE H 220 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE H 431 " --> pdb=" O MET H 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET H 454 " --> pdb=" O PHE H 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG H 433 " --> pdb=" O PHE H 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU H 451 " --> pdb=" O LEU H 462 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 327 through 333 Processing sheet with id= 25, first strand: chain 'I' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG I 25 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 163 " --> pdb=" O ARG I 25 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS I 186 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER I 32 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS I 192 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER I 199 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE I 222 " --> pdb=" O SER I 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG I 201 " --> pdb=" O PHE I 220 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 267 through 272 removed outlier: 13.275A pdb=" N PHE I 431 " --> pdb=" O MET I 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET I 454 " --> pdb=" O PHE I 431 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG I 433 " --> pdb=" O PHE I 452 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU I 451 " --> pdb=" O LEU I 462 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 327 through 333 Processing sheet with id= 28, first strand: chain 'J' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG J 25 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR J 163 " --> pdb=" O ARG J 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS J 186 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER J 32 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS J 192 " --> pdb=" O SER J 32 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N SER J 199 " --> pdb=" O ILE J 222 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ILE J 222 " --> pdb=" O SER J 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG J 201 " --> pdb=" O PHE J 220 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE J 431 " --> pdb=" O MET J 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET J 454 " --> pdb=" O PHE J 431 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG J 433 " --> pdb=" O PHE J 452 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU J 451 " --> pdb=" O LEU J 462 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 327 through 333 Processing sheet with id= 31, first strand: chain 'K' and resid 87 through 93 removed outlier: 4.171A pdb=" N ARG K 25 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR K 163 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS K 186 " --> pdb=" O PRO K 26 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER K 32 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS K 192 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER K 199 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE K 222 " --> pdb=" O SER K 199 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG K 201 " --> pdb=" O PHE K 220 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 267 through 272 removed outlier: 13.275A pdb=" N PHE K 431 " --> pdb=" O MET K 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET K 454 " --> pdb=" O PHE K 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG K 433 " --> pdb=" O PHE K 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU K 451 " --> pdb=" O LEU K 462 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 327 through 333 Processing sheet with id= 34, first strand: chain 'L' and resid 87 through 93 removed outlier: 4.172A pdb=" N ARG L 25 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR L 163 " --> pdb=" O ARG L 25 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS L 186 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER L 32 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS L 192 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N SER L 199 " --> pdb=" O ILE L 222 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE L 222 " --> pdb=" O SER L 199 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG L 201 " --> pdb=" O PHE L 220 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 267 through 272 removed outlier: 13.274A pdb=" N PHE L 431 " --> pdb=" O MET L 454 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N MET L 454 " --> pdb=" O PHE L 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG L 433 " --> pdb=" O PHE L 452 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU L 451 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 327 through 333 3000 hydrogen bonds defined for protein. 8964 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: 39.52 Time building geometry restraints manager: 62.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.57 - 0.82: 56 0.82 - 1.07: 50947 1.07 - 1.31: 8980 1.31 - 1.56: 43181 1.56 - 1.81: 492 Bond restraints: 103656 Sorted by residual: bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.85e+02 bond pdb=" C2' ATP I 601 " pdb=" C3' ATP I 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.84e+02 bond pdb=" C2' ATP J 601 " pdb=" C3' ATP J 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP H 601 " pdb=" C3' ATP H 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.82e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.82e+02 ... (remaining 103651 not shown) Histogram of bond angle deviations from ideal: 37.29 - 63.46: 51 63.46 - 89.62: 614 89.62 - 115.79: 130868 115.79 - 141.95: 55281 141.95 - 168.12: 38 Bond angle restraints: 186852 Sorted by residual: angle pdb=" NE ARG D 508 " pdb=" CD ARG D 508 " pdb=" HD3 ARG D 508 " ideal model delta sigma weight residual 108.00 37.29 70.71 3.00e+00 1.11e-01 5.56e+02 angle pdb="HH11 ARG A 550 " pdb=" NH1 ARG A 550 " pdb="HH12 ARG A 550 " ideal model delta sigma weight residual 120.00 56.16 63.84 3.00e+00 1.11e-01 4.53e+02 angle pdb=" CZ ARG B 508 " pdb=" NH1 ARG B 508 " pdb="HH12 ARG B 508 " ideal model delta sigma weight residual 120.00 60.28 59.72 3.00e+00 1.11e-01 3.96e+02 angle pdb=" CB MET H 331 " pdb=" CG MET H 331 " pdb=" HG3 MET H 331 " ideal model delta sigma weight residual 109.00 49.84 59.16 3.00e+00 1.11e-01 3.89e+02 angle pdb=" CB MET D 331 " pdb=" CG MET D 331 " pdb=" HG3 MET D 331 " ideal model delta sigma weight residual 109.00 50.05 58.95 3.00e+00 1.11e-01 3.86e+02 ... (remaining 186847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.23: 45780 28.23 - 56.45: 2085 56.45 - 84.68: 242 84.68 - 112.91: 25 112.91 - 141.13: 12 Dihedral angle restraints: 48144 sinusoidal: 27000 harmonic: 21144 Sorted by residual: dihedral pdb=" O1B ADP J 602 " pdb=" O3A ADP J 602 " pdb=" PB ADP J 602 " pdb=" PA ADP J 602 " ideal model delta sinusoidal sigma weight residual -60.00 81.13 -141.13 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP L 602 " pdb=" O3A ADP L 602 " pdb=" PB ADP L 602 " pdb=" PA ADP L 602 " ideal model delta sinusoidal sigma weight residual -60.00 81.12 -141.13 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PB ADP D 602 " pdb=" PA ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 81.12 -141.12 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 48141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 6797 0.062 - 0.123: 1017 0.123 - 0.185: 58 0.185 - 0.246: 48 0.246 - 0.308: 24 Chirality restraints: 7944 Sorted by residual: chirality pdb=" C2' ATP K 601 " pdb=" C1' ATP K 601 " pdb=" C3' ATP K 601 " pdb=" O2' ATP K 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2' ATP J 601 " pdb=" C1' ATP J 601 " pdb=" C3' ATP J 601 " pdb=" O2' ATP J 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2' ATP H 601 " pdb=" C1' ATP H 601 " pdb=" C3' ATP H 601 " pdb=" O2' ATP H 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 7941 not shown) Planarity restraints: 15648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 264 " 0.051 9.50e-02 1.11e+02 1.67e-01 6.21e+02 pdb=" NE ARG L 264 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG L 264 " -0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG L 264 " -0.180 2.00e-02 2.50e+03 pdb=" NH2 ARG L 264 " -0.236 2.00e-02 2.50e+03 pdb="HH11 ARG L 264 " 0.123 2.00e-02 2.50e+03 pdb="HH12 ARG L 264 " 0.047 2.00e-02 2.50e+03 pdb="HH21 ARG L 264 " -0.042 2.00e-02 2.50e+03 pdb="HH22 ARG L 264 " 0.349 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 508 " 0.475 9.50e-02 1.11e+02 2.11e-01 4.62e+02 pdb=" NE ARG I 508 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG I 508 " 0.137 2.00e-02 2.50e+03 pdb=" NH1 ARG I 508 " 0.191 2.00e-02 2.50e+03 pdb=" NH2 ARG I 508 " 0.031 2.00e-02 2.50e+03 pdb="HH11 ARG I 508 " 0.053 2.00e-02 2.50e+03 pdb="HH12 ARG I 508 " -0.329 2.00e-02 2.50e+03 pdb="HH21 ARG I 508 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG I 508 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 508 " -0.374 9.50e-02 1.11e+02 1.82e-01 4.15e+02 pdb=" NE ARG A 508 " 0.136 2.00e-02 2.50e+03 pdb=" CZ ARG A 508 " -0.130 2.00e-02 2.50e+03 pdb=" NH1 ARG A 508 " -0.213 2.00e-02 2.50e+03 pdb=" NH2 ARG A 508 " -0.053 2.00e-02 2.50e+03 pdb="HH11 ARG A 508 " -0.017 2.00e-02 2.50e+03 pdb="HH12 ARG A 508 " 0.273 2.00e-02 2.50e+03 pdb="HH21 ARG A 508 " 0.037 2.00e-02 2.50e+03 pdb="HH22 ARG A 508 " -0.016 2.00e-02 2.50e+03 ... (remaining 15645 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 331 1.75 - 2.46: 64698 2.46 - 3.18: 309188 3.18 - 3.89: 405644 3.89 - 4.60: 658916 Nonbonded interactions: 1438777 Sorted by model distance: nonbonded pdb=" HD3 LYS K 528 " pdb=" HE3 LYS K 528 " model vdw 1.041 1.952 nonbonded pdb=" HG3 ARG D 508 " pdb=" HD3 ARG D 508 " model vdw 1.182 1.952 nonbonded pdb=" HB3 LYS L 528 " pdb=" HG2 LYS L 528 " model vdw 1.182 1.952 nonbonded pdb=" HG3 ARG D 550 " pdb=" HD3 ARG D 550 " model vdw 1.203 1.952 nonbonded pdb=" HD3 LYS C 528 " pdb=" HE2 LYS C 528 " model vdw 1.246 1.952 ... (remaining 1438772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.620 Construct map_model_manager: 1.160 Extract box with map and model: 15.270 Check model and map are aligned: 1.160 Set scattering table: 0.710 Process input model: 254.060 Find NCS groups from input model: 3.960 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.012 0.290 52596 Z= 0.778 Angle : 1.399 27.910 71052 Z= 0.722 Chirality : 0.049 0.308 7944 Planarity : 0.012 0.227 9276 Dihedral : 15.287 141.135 19956 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.04 % Allowed : 1.73 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.65 (0.10), residues: 6528 helix: 1.40 (0.10), residues: 2844 sheet: 0.33 (0.14), residues: 1332 loop : -0.62 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 155 HIS 0.007 0.001 HIS A 401 PHE 0.030 0.002 PHE K 330 TYR 0.009 0.002 TYR I 436 ARG 0.067 0.002 ARG J 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 930 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 822 time to evaluate : 6.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 298 TYR cc_start: 0.8456 (t80) cc_final: 0.8222 (t80) REVERT: E 109 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: E 175 THR cc_start: 0.9005 (m) cc_final: 0.8720 (p) REVERT: E 532 GLU cc_start: 0.8086 (tp30) cc_final: 0.7839 (tp30) REVERT: F 109 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: G 63 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8046 (mt-10) REVERT: G 109 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: K 109 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: L 109 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6801 (pm20) outliers start: 108 outliers final: 6 residues processed: 858 average time/residue: 3.3459 time to fit residues: 3503.0101 Evaluate side-chains 464 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 453 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 510 ARG Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain J residue 297 MET Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 132 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 0.9990 chunk 491 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 331 optimal weight: 0.6980 chunk 262 optimal weight: 6.9990 chunk 507 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 chunk 588 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 401 HIS C 428 ASN C 504 GLN D 401 HIS D 428 ASN E 504 GLN F 428 ASN F 465 HIS G 401 HIS G 428 ASN H 428 ASN I 428 ASN K 504 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52596 Z= 0.210 Angle : 0.745 35.500 71052 Z= 0.359 Chirality : 0.060 1.714 7944 Planarity : 0.006 0.105 9276 Dihedral : 10.008 120.680 7833 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.09 % Allowed : 8.65 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.18 (0.10), residues: 6528 helix: 1.86 (0.09), residues: 2928 sheet: 0.70 (0.14), residues: 1308 loop : -0.54 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 322 HIS 0.005 0.001 HIS L 401 PHE 0.009 0.001 PHE I 44 TYR 0.010 0.001 TYR F 436 ARG 0.023 0.001 ARG K 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 639 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 528 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6836 (ttt90) REVERT: A 542 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8013 (mt) REVERT: B 532 GLU cc_start: 0.7802 (tp30) cc_final: 0.7542 (tp30) REVERT: C 520 LEU cc_start: 0.8255 (tt) cc_final: 0.7847 (tt) REVERT: D 131 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8706 (p) REVERT: E 131 THR cc_start: 0.8970 (m) cc_final: 0.8643 (p) REVERT: E 352 MET cc_start: 0.8100 (mtp) cc_final: 0.7876 (mtm) REVERT: E 413 GLU cc_start: 0.7158 (pt0) cc_final: 0.6776 (mp0) REVERT: E 532 GLU cc_start: 0.8059 (tp30) cc_final: 0.7850 (tp30) REVERT: E 541 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7550 (ttp80) REVERT: F 109 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: F 131 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (p) REVERT: F 331 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: G 331 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7271 (mtp) REVERT: H 539 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6781 (ttp80) REVERT: I 413 GLU cc_start: 0.7165 (pt0) cc_final: 0.6955 (mm-30) REVERT: J 131 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8748 (p) REVERT: J 517 GLU cc_start: 0.7674 (tt0) cc_final: 0.7151 (tm-30) REVERT: K 106 TYR cc_start: 0.6435 (t80) cc_final: 0.6023 (t80) REVERT: K 131 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8652 (p) REVERT: K 541 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7521 (ptm-80) REVERT: L 106 TYR cc_start: 0.6388 (t80) cc_final: 0.6051 (t80) REVERT: L 131 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8710 (p) outliers start: 111 outliers final: 16 residues processed: 590 average time/residue: 3.0622 time to fit residues: 2251.9199 Evaluate side-chains 489 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 462 time to evaluate : 5.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 517 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 539 ARG Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain L residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 489 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 589 optimal weight: 8.9990 chunk 636 optimal weight: 5.9990 chunk 525 optimal weight: 4.9990 chunk 584 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 472 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 401 HIS C 428 ASN C 504 GLN D 401 HIS D 428 ASN D 500 GLN E 504 GLN F 465 HIS G 401 HIS G 428 ASN H 428 ASN H 432 ASN I 428 ASN K 465 HIS K 504 GLN L 465 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 52596 Z= 0.412 Angle : 0.696 30.841 71052 Z= 0.346 Chirality : 0.063 1.816 7944 Planarity : 0.004 0.073 9276 Dihedral : 9.430 103.569 7803 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.79 % Allowed : 9.45 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.28 (0.10), residues: 6528 helix: 1.95 (0.09), residues: 2964 sheet: 0.42 (0.13), residues: 1416 loop : -0.35 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 322 HIS 0.006 0.001 HIS J 398 PHE 0.015 0.002 PHE A 44 TYR 0.012 0.002 TYR H 208 ARG 0.010 0.001 ARG K 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 593 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 498 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.8788 (t80) cc_final: 0.7848 (t80) REVERT: A 542 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7963 (mt) REVERT: B 62 GLU cc_start: 0.8138 (tp30) cc_final: 0.7794 (tp30) REVERT: B 331 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7331 (mtp) REVERT: C 520 LEU cc_start: 0.8385 (tt) cc_final: 0.8075 (tt) REVERT: E 517 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: F 428 ASN cc_start: 0.7955 (t0) cc_final: 0.7699 (t0) REVERT: G 331 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7231 (mtp) REVERT: G 428 ASN cc_start: 0.7961 (t0) cc_final: 0.7661 (t0) REVERT: H 298 TYR cc_start: 0.8795 (t80) cc_final: 0.7890 (t80) REVERT: I 116 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: I 298 TYR cc_start: 0.8895 (t80) cc_final: 0.8012 (t80) REVERT: I 520 LEU cc_start: 0.8393 (tt) cc_final: 0.8165 (tt) REVERT: J 331 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7006 (mtp) REVERT: K 106 TYR cc_start: 0.6566 (t80) cc_final: 0.6169 (t80) REVERT: K 541 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7650 (ttp80) REVERT: L 106 TYR cc_start: 0.6541 (t80) cc_final: 0.6154 (t80) REVERT: L 541 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7691 (ttp80) outliers start: 95 outliers final: 20 residues processed: 557 average time/residue: 2.9112 time to fit residues: 2055.1209 Evaluate side-chains 473 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 447 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 517 GLU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 500 GLN Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 413 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 4.9990 chunk 443 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 395 optimal weight: 5.9990 chunk 591 optimal weight: 5.9990 chunk 626 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 560 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 401 HIS D 401 HIS D 428 ASN D 432 ASN E 504 GLN G 401 HIS H 428 ASN H 504 GLN I 428 ASN K 504 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 52596 Z= 0.372 Angle : 0.667 35.650 71052 Z= 0.328 Chirality : 0.063 1.807 7944 Planarity : 0.004 0.101 9276 Dihedral : 9.218 110.560 7800 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.94 % Allowed : 9.63 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.49 (0.10), residues: 6528 helix: 2.13 (0.09), residues: 2964 sheet: 0.35 (0.13), residues: 1416 loop : -0.12 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 322 HIS 0.005 0.001 HIS K 398 PHE 0.014 0.002 PHE H 44 TYR 0.012 0.002 TYR H 208 ARG 0.005 0.000 ARG E 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 600 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 497 time to evaluate : 6.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.8785 (t80) cc_final: 0.7741 (t80) REVERT: A 514 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 62 GLU cc_start: 0.8063 (tp30) cc_final: 0.7821 (tp30) REVERT: B 331 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: B 519 GLU cc_start: 0.7730 (tt0) cc_final: 0.7391 (tm-30) REVERT: D 331 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: D 428 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7864 (t0) REVERT: D 454 MET cc_start: 0.8765 (mtt) cc_final: 0.8524 (mtt) REVERT: G 331 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: G 428 ASN cc_start: 0.8062 (t0) cc_final: 0.7757 (t0) REVERT: H 298 TYR cc_start: 0.8781 (t80) cc_final: 0.7710 (t80) REVERT: I 298 TYR cc_start: 0.8864 (t80) cc_final: 0.7833 (t80) REVERT: I 520 LEU cc_start: 0.8454 (tt) cc_final: 0.8250 (tt) REVERT: J 519 GLU cc_start: 0.7706 (tt0) cc_final: 0.7409 (tm-30) REVERT: K 541 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7797 (ttp80) REVERT: L 541 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7727 (ttp80) outliers start: 103 outliers final: 39 residues processed: 553 average time/residue: 2.7857 time to fit residues: 1960.3533 Evaluate side-chains 505 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 461 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 428 ASN Chi-restraints excluded: chain I residue 514 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 414 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 466 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 534 optimal weight: 10.0000 chunk 432 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 562 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 HIS C 428 ASN D 401 HIS D 428 ASN E 504 GLN G 401 HIS H 504 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 52596 Z= 0.434 Angle : 0.651 30.886 71052 Z= 0.329 Chirality : 0.063 1.794 7944 Planarity : 0.004 0.061 9276 Dihedral : 9.277 111.675 7800 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.04 % Allowed : 10.24 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.44 (0.10), residues: 6528 helix: 2.12 (0.09), residues: 2964 sheet: 0.29 (0.13), residues: 1416 loop : -0.13 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 322 HIS 0.006 0.001 HIS J 398 PHE 0.014 0.002 PHE I 44 TYR 0.011 0.002 TYR H 208 ARG 0.005 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 603 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 495 time to evaluate : 6.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLU cc_start: 0.8130 (tp30) cc_final: 0.7887 (tp30) REVERT: B 331 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: D 331 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7049 (mtp) REVERT: G 331 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7248 (mtp) REVERT: G 428 ASN cc_start: 0.8110 (t0) cc_final: 0.7890 (t0) REVERT: G 454 MET cc_start: 0.8846 (mtt) cc_final: 0.8561 (mtt) REVERT: H 298 TYR cc_start: 0.8804 (t80) cc_final: 0.7737 (t80) REVERT: I 298 TYR cc_start: 0.8890 (t80) cc_final: 0.7770 (t80) REVERT: J 519 GLU cc_start: 0.7603 (tt0) cc_final: 0.7285 (tm-30) outliers start: 108 outliers final: 46 residues processed: 562 average time/residue: 2.7907 time to fit residues: 2003.7507 Evaluate side-chains 508 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 459 time to evaluate : 5.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 502 ILE Chi-restraints excluded: chain I residue 514 GLU Chi-restraints excluded: chain I residue 533 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 500 GLN Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 414 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 8.9990 chunk 564 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 626 optimal weight: 4.9990 chunk 520 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 329 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 HIS B 432 ASN C 401 HIS D 401 HIS E 504 GLN F 432 ASN G 401 HIS G 432 ASN H 504 GLN J 401 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 52596 Z= 0.247 Angle : 0.589 22.484 71052 Z= 0.295 Chirality : 0.061 1.788 7944 Planarity : 0.004 0.089 9276 Dihedral : 8.912 106.950 7800 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.81 % Allowed : 11.01 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.71 (0.10), residues: 6528 helix: 2.43 (0.09), residues: 2952 sheet: 0.42 (0.13), residues: 1392 loop : -0.12 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 322 HIS 0.004 0.001 HIS J 398 PHE 0.012 0.001 PHE I 44 TYR 0.008 0.001 TYR D 436 ARG 0.004 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 595 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 499 time to evaluate : 6.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.8805 (t80) cc_final: 0.7623 (t80) REVERT: B 62 GLU cc_start: 0.8052 (tp30) cc_final: 0.7824 (tp30) REVERT: B 331 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: B 454 MET cc_start: 0.8805 (mtt) cc_final: 0.8601 (mtt) REVERT: C 434 GLU cc_start: 0.7744 (mp0) cc_final: 0.7503 (mp0) REVERT: C 514 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 517 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: G 331 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7275 (mtp) REVERT: G 428 ASN cc_start: 0.8012 (t0) cc_final: 0.7785 (t0) REVERT: G 454 MET cc_start: 0.8842 (mtt) cc_final: 0.8628 (mtt) REVERT: G 517 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 298 TYR cc_start: 0.8782 (t80) cc_final: 0.7606 (t80) REVERT: H 514 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: I 298 TYR cc_start: 0.8881 (t80) cc_final: 0.7720 (t80) REVERT: I 514 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: J 517 GLU cc_start: 0.7886 (tt0) cc_final: 0.7461 (tm-30) outliers start: 96 outliers final: 48 residues processed: 558 average time/residue: 2.7626 time to fit residues: 1966.9040 Evaluate side-chains 527 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 473 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 413 GLU Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 502 ILE Chi-restraints excluded: chain I residue 514 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 502 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 414 GLU Chi-restraints excluded: chain L residue 502 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 457 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 527 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 624 optimal weight: 6.9990 chunk 390 optimal weight: 4.9990 chunk 380 optimal weight: 0.6980 chunk 288 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 HIS C 401 HIS D 401 HIS E 504 GLN F 428 ASN G 401 HIS I 428 ASN J 401 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 52596 Z= 0.326 Angle : 0.600 22.337 71052 Z= 0.302 Chirality : 0.062 1.784 7944 Planarity : 0.004 0.042 9276 Dihedral : 8.848 107.936 7800 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.73 % Allowed : 11.12 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.67 (0.10), residues: 6528 helix: 2.42 (0.09), residues: 2952 sheet: 0.27 (0.13), residues: 1416 loop : -0.09 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 322 HIS 0.032 0.001 HIS C 401 PHE 0.012 0.001 PHE A 44 TYR 0.009 0.002 TYR C 208 ARG 0.005 0.000 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 584 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 492 time to evaluate : 6.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLU cc_start: 0.8067 (tp30) cc_final: 0.7845 (tp30) REVERT: B 331 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7288 (mtp) REVERT: B 454 MET cc_start: 0.8838 (mtt) cc_final: 0.8612 (mtt) REVERT: C 514 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: D 517 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: G 331 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7296 (mtp) REVERT: G 428 ASN cc_start: 0.8031 (t0) cc_final: 0.7797 (t0) REVERT: G 454 MET cc_start: 0.8867 (mtt) cc_final: 0.8636 (mtt) REVERT: G 517 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7694 (tm-30) REVERT: I 298 TYR cc_start: 0.8912 (t80) cc_final: 0.7745 (t80) REVERT: J 517 GLU cc_start: 0.7889 (tt0) cc_final: 0.7483 (tm-30) REVERT: J 527 LEU cc_start: 0.8488 (mm) cc_final: 0.8279 (mm) outliers start: 92 outliers final: 43 residues processed: 555 average time/residue: 2.7085 time to fit residues: 1930.8865 Evaluate side-chains 517 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 470 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 502 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 502 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 414 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 373 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 397 optimal weight: 3.9990 chunk 425 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 490 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS A 428 ASN B 401 HIS C 401 HIS D 401 HIS E 504 GLN F 428 ASN G 401 HIS H 401 HIS I 401 HIS J 401 HIS K 192 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 52596 Z= 0.326 Angle : 0.598 22.610 71052 Z= 0.301 Chirality : 0.061 1.757 7944 Planarity : 0.004 0.113 9276 Dihedral : 8.721 108.118 7800 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.73 % Allowed : 11.56 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.69 (0.10), residues: 6528 helix: 2.42 (0.09), residues: 2964 sheet: 0.26 (0.13), residues: 1416 loop : -0.04 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 322 HIS 0.007 0.001 HIS C 401 PHE 0.013 0.001 PHE I 44 TYR 0.013 0.002 TYR I 208 ARG 0.009 0.000 ARG G 550 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 576 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 484 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: C 514 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: G 331 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: G 428 ASN cc_start: 0.8055 (t0) cc_final: 0.7855 (t0) REVERT: G 454 MET cc_start: 0.8849 (mtt) cc_final: 0.8596 (mtt) REVERT: G 517 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7667 (tm-30) REVERT: H 514 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: I 298 TYR cc_start: 0.8888 (t80) cc_final: 0.7714 (t80) REVERT: I 514 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: J 517 GLU cc_start: 0.7887 (tt0) cc_final: 0.7487 (tm-30) outliers start: 92 outliers final: 47 residues processed: 543 average time/residue: 2.6894 time to fit residues: 1875.9855 Evaluate side-chains 524 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 472 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 514 GLU Chi-restraints excluded: chain I residue 533 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 502 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 524 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 414 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 5.9990 chunk 598 optimal weight: 0.8980 chunk 545 optimal weight: 0.9980 chunk 582 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 457 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 525 optimal weight: 3.9990 chunk 550 optimal weight: 9.9990 chunk 579 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS B 401 HIS C 401 HIS C 432 ASN D 401 HIS G 401 HIS H 401 HIS I 401 HIS J 401 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 52596 Z= 0.203 Angle : 0.572 22.506 71052 Z= 0.284 Chirality : 0.061 1.767 7944 Planarity : 0.004 0.056 9276 Dihedral : 8.437 103.067 7800 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.32 % Allowed : 12.07 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.87 (0.10), residues: 6528 helix: 2.64 (0.09), residues: 2952 sheet: 0.27 (0.13), residues: 1416 loop : -0.01 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 322 HIS 0.026 0.001 HIS H 401 PHE 0.011 0.001 PHE A 44 TYR 0.009 0.001 TYR I 208 ARG 0.007 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 548 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 478 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 428 ASN cc_start: 0.8015 (t0) cc_final: 0.7814 (t0) REVERT: I 298 TYR cc_start: 0.8876 (t80) cc_final: 0.7711 (t80) REVERT: J 264 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6506 (mtp-110) REVERT: J 517 GLU cc_start: 0.7866 (tt0) cc_final: 0.7441 (tm-30) REVERT: L 519 GLU cc_start: 0.7679 (tt0) cc_final: 0.7257 (tm-30) outliers start: 70 outliers final: 36 residues processed: 525 average time/residue: 2.6819 time to fit residues: 1814.8092 Evaluate side-chains 499 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 462 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 264 ARG Chi-restraints excluded: chain J residue 502 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 524 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 414 GLU Chi-restraints excluded: chain L residue 524 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 0.7980 chunk 615 optimal weight: 1.9990 chunk 375 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 427 optimal weight: 0.5980 chunk 645 optimal weight: 8.9990 chunk 594 optimal weight: 0.6980 chunk 514 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 397 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS B 401 HIS C 401 HIS D 401 HIS D 500 GLN E 432 ASN G 401 HIS H 401 HIS I 401 HIS I 432 ASN J 401 HIS J 432 ASN J 500 GLN L 432 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 52596 Z= 0.151 Angle : 0.552 22.130 71052 Z= 0.270 Chirality : 0.061 1.776 7944 Planarity : 0.004 0.082 9276 Dihedral : 8.010 89.870 7800 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.81 % Allowed : 12.71 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.06 (0.11), residues: 6528 helix: 2.70 (0.09), residues: 3024 sheet: 0.41 (0.13), residues: 1392 loop : 0.11 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 322 HIS 0.005 0.001 HIS C 401 PHE 0.008 0.001 PHE A 220 TYR 0.009 0.001 TYR F 436 ARG 0.020 0.000 ARG L 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13056 Ramachandran restraints generated. 6528 Oldfield, 0 Emsley, 6528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue SER 279 is missing expected H atoms. Skipping. Evaluate side-chains 538 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 495 time to evaluate : 6.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 434 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7794 (mp0) REVERT: G 428 ASN cc_start: 0.7925 (t0) cc_final: 0.7724 (t0) REVERT: I 298 TYR cc_start: 0.8868 (t80) cc_final: 0.7601 (t80) REVERT: J 131 THR cc_start: 0.9182 (m) cc_final: 0.8963 (p) REVERT: J 517 GLU cc_start: 0.7794 (tt0) cc_final: 0.7403 (tm-30) REVERT: K 519 GLU cc_start: 0.7724 (tt0) cc_final: 0.7407 (tm-30) REVERT: L 414 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: L 519 GLU cc_start: 0.7678 (tt0) cc_final: 0.7365 (tm-30) outliers start: 43 outliers final: 22 residues processed: 523 average time/residue: 2.6280 time to fit residues: 1781.0458 Evaluate side-chains 488 residues out of total 5304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 465 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 242 HIS Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 413 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 524 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 414 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 4.9990 chunk 547 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 474 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 514 optimal weight: 0.0970 chunk 215 optimal weight: 0.8980 chunk 528 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS B 401 HIS ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS D 401 HIS ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 499 GLN F 401 HIS G 401 HIS G 500 GLN H 401 HIS I 401 HIS J 401 HIS J 500 GLN L 401 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099170 restraints weight = 230277.920| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.80 r_work: 0.3221 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 52596 Z= 0.284 Angle : 0.578 22.396 71052 Z= 0.286 Chirality : 0.061 1.788 7944 Planarity : 0.004 0.052 9276 Dihedral : 8.227 98.860 7800 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.00 % Allowed : 12.80 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.90 (0.10), residues: 6528 helix: 2.58 (0.09), residues: 3024 sheet: 0.24 (0.13), residues: 1416 loop : 0.08 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 322 HIS 0.005 0.001 HIS C 401 PHE 0.011 0.001 PHE I 44 TYR 0.013 0.001 TYR I 208 ARG 0.006 0.000 ARG D 550 =============================================================================== Job complete usr+sys time: 29798.29 seconds wall clock time: 509 minutes 49.63 seconds (30589.63 seconds total)