Starting phenix.real_space_refine on Mon Nov 18 19:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/11_2024/6z1f_11028.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 12 5.21 5 S 182 5.16 5 C 31680 2.51 5 N 8613 2.21 5 O 9297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 213 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49815 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2184 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 264} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "2" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2215 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "3" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2241 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 268} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2222 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2206 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 264} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2174 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3665 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3601 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'KCX:plan-1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 30.20, per 1000 atoms: 0.61 Number of scatterers: 49815 At special positions: 0 Unit cell: (145.555, 199.181, 163.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 31 15.00 Mg 12 11.99 O 9297 8.00 N 8613 7.00 C 31680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS B 248 " distance=2.05 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS D 248 " distance=2.04 Simple disulfide: pdb=" SG CYS E 248 " - pdb=" SG CYS F 248 " distance=2.04 Simple disulfide: pdb=" SG CYS G 248 " - pdb=" SG CYS H 248 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 5.9 seconds 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11500 Finding SS restraints... Secondary structure from input PDB file: 259 helices and 39 sheets defined 47.9% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain '1' and resid 6 through 22 Processing helix chain '1' and resid 42 through 55 Processing helix chain '1' and resid 62 through 66 removed outlier: 3.703A pdb=" N LEU 1 66 " --> pdb=" O GLY 1 63 " (cutoff:3.500A) Processing helix chain '1' and resid 73 through 93 removed outlier: 3.849A pdb=" N ARG 1 79 " --> pdb=" O ALA 1 75 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE 1 89 " --> pdb=" O THR 1 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS 1 90 " --> pdb=" O ALA 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 117 through 133 Processing helix chain '1' and resid 161 through 163 No H-bonds generated for 'chain '1' and resid 161 through 163' Processing helix chain '1' and resid 164 through 170 Processing helix chain '1' and resid 181 through 193 Processing helix chain '1' and resid 199 through 210 Processing helix chain '1' and resid 214 through 221 removed outlier: 4.169A pdb=" N PHE 1 218 " --> pdb=" O SER 1 214 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER 1 219 " --> pdb=" O ILE 1 215 " (cutoff:3.500A) Processing helix chain '1' and resid 222 through 224 No H-bonds generated for 'chain '1' and resid 222 through 224' Processing helix chain '1' and resid 226 through 238 removed outlier: 3.649A pdb=" N HIS 1 235 " --> pdb=" O ARG 1 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 1 236 " --> pdb=" O ASP 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 241 No H-bonds generated for 'chain '1' and resid 239 through 241' Processing helix chain '1' and resid 242 through 248 removed outlier: 3.774A pdb=" N VAL 1 246 " --> pdb=" O ILE 1 242 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN 1 248 " --> pdb=" O LEU 1 244 " (cutoff:3.500A) Processing helix chain '1' and resid 262 through 281 removed outlier: 3.657A pdb=" N LEU 1 266 " --> pdb=" O SER 1 262 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 22 removed outlier: 3.646A pdb=" N HIS 2 16 " --> pdb=" O LYS 2 12 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 2 21 " --> pdb=" O ILE 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 54 removed outlier: 3.732A pdb=" N CYS 2 47 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET 2 54 " --> pdb=" O ALA 2 50 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 66 removed outlier: 3.891A pdb=" N GLU 2 65 " --> pdb=" O SER 2 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 2 66 " --> pdb=" O GLY 2 63 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 62 through 66' Processing helix chain '2' and resid 72 through 93 removed outlier: 3.551A pdb=" N ILE 2 78 " --> pdb=" O PRO 2 74 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG 2 79 " --> pdb=" O ALA 2 75 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE 2 89 " --> pdb=" O THR 2 85 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS 2 90 " --> pdb=" O ALA 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 131 removed outlier: 3.614A pdb=" N ASN 2 124 " --> pdb=" O THR 2 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 129 " --> pdb=" O ALA 2 125 " (cutoff:3.500A) Processing helix chain '2' and resid 164 through 168 Processing helix chain '2' and resid 181 through 193 Processing helix chain '2' and resid 199 through 210 removed outlier: 3.529A pdb=" N PHE 2 210 " --> pdb=" O LEU 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 225 removed outlier: 3.791A pdb=" N SER 2 219 " --> pdb=" O ILE 2 215 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 2 221 " --> pdb=" O PHE 2 217 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 238 Processing helix chain '2' and resid 239 through 242 removed outlier: 3.935A pdb=" N ILE 2 242 " --> pdb=" O PHE 2 239 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 239 through 242' Processing helix chain '2' and resid 262 through 282 Processing helix chain '3' and resid 6 through 22 removed outlier: 3.537A pdb=" N ASN 3 20 " --> pdb=" O HIS 3 16 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE 3 21 " --> pdb=" O ILE 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 55 removed outlier: 3.678A pdb=" N GLN 3 46 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS 3 47 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU 3 52 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 66 removed outlier: 3.599A pdb=" N GLU 3 65 " --> pdb=" O SER 3 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 3 66 " --> pdb=" O GLY 3 63 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 62 through 66' Processing helix chain '3' and resid 73 through 93 removed outlier: 3.659A pdb=" N ILE 3 78 " --> pdb=" O PRO 3 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG 3 79 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 3 88 " --> pdb=" O GLU 3 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE 3 89 " --> pdb=" O THR 3 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS 3 90 " --> pdb=" O ALA 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 133 removed outlier: 4.201A pdb=" N GLN 3 121 " --> pdb=" O THR 3 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET 3 128 " --> pdb=" O ASN 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 164 through 168 Processing helix chain '3' and resid 181 through 193 Processing helix chain '3' and resid 199 through 210 removed outlier: 3.541A pdb=" N VAL 3 207 " --> pdb=" O ILE 3 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE 3 210 " --> pdb=" O LEU 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 222 removed outlier: 3.612A pdb=" N SER 3 219 " --> pdb=" O ILE 3 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG 3 222 " --> pdb=" O PHE 3 218 " (cutoff:3.500A) Processing helix chain '3' and resid 226 through 238 Processing helix chain '3' and resid 239 through 246 removed outlier: 3.915A pdb=" N ILE 3 242 " --> pdb=" O PHE 3 239 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER 3 243 " --> pdb=" O GLU 3 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 3 244 " --> pdb=" O ARG 3 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG 3 245 " --> pdb=" O ILE 3 242 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 3 246 " --> pdb=" O SER 3 243 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 239 through 246' Processing helix chain '3' and resid 262 through 282 removed outlier: 3.835A pdb=" N VAL 3 280 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 22 removed outlier: 3.636A pdb=" N HIS 4 16 " --> pdb=" O LYS 4 12 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN 4 20 " --> pdb=" O HIS 4 16 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE 4 21 " --> pdb=" O ILE 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 55 removed outlier: 3.658A pdb=" N GLN 4 46 " --> pdb=" O GLY 4 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS 4 47 " --> pdb=" O LYS 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 62 through 66 removed outlier: 3.511A pdb=" N GLU 4 65 " --> pdb=" O SER 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 72 through 93 removed outlier: 3.633A pdb=" N ARG 4 76 " --> pdb=" O GLY 4 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG 4 79 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE 4 89 " --> pdb=" O THR 4 85 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS 4 90 " --> pdb=" O ALA 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 103 through 108 Processing helix chain '4' and resid 117 through 131 removed outlier: 4.144A pdb=" N GLN 4 121 " --> pdb=" O THR 4 117 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN 4 124 " --> pdb=" O THR 4 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 4 128 " --> pdb=" O ASN 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 164 through 168 Processing helix chain '4' and resid 181 through 193 Processing helix chain '4' and resid 199 through 210 removed outlier: 3.604A pdb=" N PHE 4 210 " --> pdb=" O LEU 4 206 " (cutoff:3.500A) Processing helix chain '4' and resid 214 through 226 removed outlier: 4.167A pdb=" N PHE 4 218 " --> pdb=" O SER 4 214 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 4 221 " --> pdb=" O PHE 4 217 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG 4 222 " --> pdb=" O PHE 4 218 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER 4 223 " --> pdb=" O SER 4 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 4 224 " --> pdb=" O ALA 4 220 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR 4 226 " --> pdb=" O ARG 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 238 Processing helix chain '4' and resid 239 through 242 removed outlier: 3.793A pdb=" N ILE 4 242 " --> pdb=" O PHE 4 239 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 239 through 242' Processing helix chain '4' and resid 262 through 282 removed outlier: 3.741A pdb=" N VAL 4 280 " --> pdb=" O GLU 4 276 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 22 removed outlier: 3.675A pdb=" N ASN 5 20 " --> pdb=" O HIS 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 55 Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 72 through 93 removed outlier: 3.513A pdb=" N ILE 5 78 " --> pdb=" O PRO 5 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG 5 79 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 5 83 " --> pdb=" O ARG 5 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 5 88 " --> pdb=" O GLU 5 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE 5 89 " --> pdb=" O THR 5 85 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS 5 90 " --> pdb=" O ALA 5 86 " (cutoff:3.500A) Processing helix chain '5' and resid 118 through 133 removed outlier: 3.555A pdb=" N ALA 5 125 " --> pdb=" O GLN 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 164 through 168 Processing helix chain '5' and resid 181 through 193 Processing helix chain '5' and resid 199 through 210 removed outlier: 3.574A pdb=" N PHE 5 210 " --> pdb=" O LEU 5 206 " (cutoff:3.500A) Processing helix chain '5' and resid 214 through 226 removed outlier: 4.289A pdb=" N PHE 5 218 " --> pdb=" O SER 5 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER 5 219 " --> pdb=" O ILE 5 215 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG 5 222 " --> pdb=" O PHE 5 218 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER 5 223 " --> pdb=" O SER 5 219 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 5 224 " --> pdb=" O ALA 5 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 5 225 " --> pdb=" O LEU 5 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR 5 226 " --> pdb=" O ARG 5 222 " (cutoff:3.500A) Processing helix chain '5' and resid 226 through 238 Processing helix chain '5' and resid 241 through 248 removed outlier: 3.985A pdb=" N ARG 5 245 " --> pdb=" O ARG 5 241 " (cutoff:3.500A) Processing helix chain '5' and resid 262 through 281 removed outlier: 3.784A pdb=" N VAL 5 280 " --> pdb=" O GLU 5 276 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 22 Processing helix chain '6' and resid 42 through 55 removed outlier: 3.775A pdb=" N CYS 6 47 " --> pdb=" O LYS 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 66 removed outlier: 3.653A pdb=" N LEU 6 66 " --> pdb=" O GLY 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 92 removed outlier: 3.642A pdb=" N ILE 6 78 " --> pdb=" O PRO 6 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 106 removed outlier: 3.887A pdb=" N ALA 6 105 " --> pdb=" O ASP 6 102 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 133 removed outlier: 4.293A pdb=" N GLN 6 121 " --> pdb=" O THR 6 117 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN 6 124 " --> pdb=" O THR 6 120 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 168 Processing helix chain '6' and resid 181 through 193 Processing helix chain '6' and resid 199 through 210 Processing helix chain '6' and resid 214 through 238 removed outlier: 3.994A pdb=" N PHE 6 218 " --> pdb=" O SER 6 214 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER 6 219 " --> pdb=" O ILE 6 215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER 6 223 " --> pdb=" O SER 6 219 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 6 228 " --> pdb=" O ARG 6 224 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN 6 229 " --> pdb=" O ILE 6 225 " (cutoff:3.500A) Processing helix chain '6' and resid 243 through 248 removed outlier: 4.307A pdb=" N ASN 6 248 " --> pdb=" O LEU 6 244 " (cutoff:3.500A) Processing helix chain '6' and resid 262 through 281 removed outlier: 3.573A pdb=" N GLU 6 268 " --> pdb=" O ALA 6 264 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY 6 270 " --> pdb=" O LEU 6 266 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 6 280 " --> pdb=" O GLU 6 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 62 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.623A pdb=" N THR A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.616A pdb=" N VAL A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.624A pdb=" N GLY A 197 " --> pdb=" O CYS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.782A pdb=" N VAL A 301 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.845A pdb=" N LEU A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.589A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.581A pdb=" N GLU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.617A pdb=" N LEU A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 435 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.563A pdb=" N ILE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 463 removed outlier: 3.633A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.915A pdb=" N SER B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.573A pdb=" N ASP B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.982A pdb=" N TYR B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.663A pdb=" N VAL B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.538A pdb=" N ASP B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.636A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 197 " --> pdb=" O CYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 234 removed outlier: 3.521A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.505A pdb=" N TYR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.691A pdb=" N ARG B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.682A pdb=" N LEU B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.714A pdb=" N GLY B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 396 Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.963A pdb=" N LEU B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 435 removed outlier: 3.582A pdb=" N ASN B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.578A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.688A pdb=" N SER C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.515A pdb=" N ASP C 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.725A pdb=" N TYR C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.709A pdb=" N VAL C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 154 through 164 removed outlier: 4.372A pdb=" N VAL C 158 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 214 through 234 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 274 through 289 Processing helix chain 'C' and resid 298 through 304 removed outlier: 4.605A pdb=" N ILE C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.711A pdb=" N LEU C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.613A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 387 through 396 removed outlier: 3.554A pdb=" N ILE C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.526A pdb=" N LEU C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 435 removed outlier: 3.588A pdb=" N GLY C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 removed outlier: 5.983A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 463 removed outlier: 3.565A pdb=" N ALA C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.685A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.517A pdb=" N ASP D 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 82 removed outlier: 3.725A pdb=" N TYR D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.707A pdb=" N VAL D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 154 through 164 removed outlier: 4.388A pdb=" N VAL D 158 " --> pdb=" O HIS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 214 through 234 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 274 through 289 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.607A pdb=" N ILE D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.716A pdb=" N LEU D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.614A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 396 removed outlier: 3.548A pdb=" N ILE D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.527A pdb=" N LEU D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 435 removed outlier: 3.581A pdb=" N GLY D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 5.980A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.569A pdb=" N ALA D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.993A pdb=" N SER E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.527A pdb=" N ASP E 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.861A pdb=" N TYR E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.834A pdb=" N VAL E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 155 through 164 removed outlier: 3.592A pdb=" N ASP E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.566A pdb=" N GLY E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY E 197 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 234 Processing helix chain 'E' and resid 247 through 261 removed outlier: 3.524A pdb=" N TYR E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 274 through 289 Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.736A pdb=" N ARG E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.745A pdb=" N LEU E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.519A pdb=" N GLY E 345 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 396 Processing helix chain 'E' and resid 404 through 409 removed outlier: 3.693A pdb=" N LEU E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 435 removed outlier: 3.544A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 450 removed outlier: 3.690A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 463 removed outlier: 3.534A pdb=" N ALA E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP E 463 " --> pdb=" O ALA E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 3.903A pdb=" N SER F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.508A pdb=" N ASP F 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 3.886A pdb=" N TYR F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.782A pdb=" N VAL F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 154 through 164 removed outlier: 4.321A pdb=" N VAL F 158 " --> pdb=" O HIS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.519A pdb=" N GLY F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY F 197 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 Processing helix chain 'F' and resid 247 through 261 removed outlier: 3.565A pdb=" N TYR F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 274 through 289 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 311 through 323 removed outlier: 3.662A pdb=" N LEU F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.537A pdb=" N GLY F 345 " --> pdb=" O GLY F 341 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 396 Processing helix chain 'F' and resid 404 through 409 removed outlier: 3.682A pdb=" N LEU F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 435 removed outlier: 3.541A pdb=" N ASN F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 450 removed outlier: 3.633A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.507A pdb=" N ALA F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.505A pdb=" N VAL G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 75 Processing helix chain 'G' and resid 77 through 82 removed outlier: 3.843A pdb=" N TYR G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.722A pdb=" N VAL G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 154 through 164 removed outlier: 4.364A pdb=" N VAL G 158 " --> pdb=" O HIS G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 197 removed outlier: 3.789A pdb=" N GLY G 197 " --> pdb=" O CYS G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 234 Processing helix chain 'G' and resid 247 through 261 Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 274 through 289 Processing helix chain 'G' and resid 299 through 304 removed outlier: 3.667A pdb=" N ARG G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 removed outlier: 3.779A pdb=" N LEU G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 removed outlier: 3.560A pdb=" N GLU G 352 " --> pdb=" O ASP G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 387 through 396 Processing helix chain 'G' and resid 404 through 409 removed outlier: 3.685A pdb=" N LEU G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 435 removed outlier: 3.568A pdb=" N GLY G 435 " --> pdb=" O ALA G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 450 removed outlier: 3.713A pdb=" N ILE G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.620A pdb=" N GLU G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP G 463 " --> pdb=" O ALA G 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 63 removed outlier: 3.921A pdb=" N SER H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 75 Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.764A pdb=" N TYR H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 113 through 122 removed outlier: 3.645A pdb=" N VAL H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 155 through 164 removed outlier: 3.624A pdb=" N ASP H 161 " --> pdb=" O GLN H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 197 removed outlier: 3.660A pdb=" N GLY H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY H 197 " --> pdb=" O CYS H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 234 Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.572A pdb=" N TYR H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 274 Processing helix chain 'H' and resid 274 through 289 Processing helix chain 'H' and resid 299 through 304 removed outlier: 3.631A pdb=" N ARG H 304 " --> pdb=" O ALA H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 323 removed outlier: 3.743A pdb=" N LEU H 315 " --> pdb=" O HIS H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 removed outlier: 3.531A pdb=" N GLY H 345 " --> pdb=" O GLY H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 396 Processing helix chain 'H' and resid 404 through 409 Processing helix chain 'H' and resid 413 through 435 removed outlier: 3.532A pdb=" N GLY H 435 " --> pdb=" O ALA H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 450 removed outlier: 3.695A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 463 removed outlier: 3.567A pdb=" N ALA H 457 " --> pdb=" O SER H 453 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP H 463 " --> pdb=" O ALA H 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 35 removed outlier: 3.553A pdb=" N ILE I 31 " --> pdb=" O GLN I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 removed outlier: 4.147A pdb=" N VAL I 69 " --> pdb=" O THR I 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 35 removed outlier: 3.514A pdb=" N ILE J 31 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 80 removed outlier: 4.083A pdb=" N VAL J 69 " --> pdb=" O THR J 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 35 removed outlier: 3.510A pdb=" N ILE K 31 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 80 removed outlier: 4.253A pdb=" N VAL K 69 " --> pdb=" O THR K 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 35 removed outlier: 3.509A pdb=" N ILE L 31 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 80 removed outlier: 4.252A pdb=" N VAL L 69 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 35 Processing helix chain 'M' and resid 66 through 80 removed outlier: 3.619A pdb=" N GLU M 72 " --> pdb=" O GLU M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 35 removed outlier: 3.540A pdb=" N ILE N 31 " --> pdb=" O GLN N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 80 removed outlier: 4.108A pdb=" N VAL N 69 " --> pdb=" O THR N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 35 Processing helix chain 'O' and resid 66 through 80 removed outlier: 3.591A pdb=" N GLU O 72 " --> pdb=" O GLU O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 35 removed outlier: 3.601A pdb=" N ILE P 31 " --> pdb=" O GLN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 80 removed outlier: 4.243A pdb=" N VAL P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 57 through 61 removed outlier: 6.517A pdb=" N GLU 1 57 " --> pdb=" O VAL 1 97 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET 1 99 " --> pdb=" O GLU 1 57 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR 1 59 " --> pdb=" O MET 1 99 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN 1 101 " --> pdb=" O THR 1 59 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE 1 61 " --> pdb=" O ASN 1 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 57 through 61 removed outlier: 6.468A pdb=" N GLU 2 57 " --> pdb=" O VAL 2 97 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET 2 99 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR 2 59 " --> pdb=" O MET 2 99 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN 2 101 " --> pdb=" O THR 2 59 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE 2 61 " --> pdb=" O ASN 2 101 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE 2 154 " --> pdb=" O CYS 2 96 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU 2 98 " --> pdb=" O ILE 2 154 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR 2 156 " --> pdb=" O LEU 2 98 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE 2 100 " --> pdb=" O THR 2 156 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY 2 37 " --> pdb=" O GLY 2 157 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE 2 32 " --> pdb=" O GLU 2 174 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE 2 176 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY 2 34 " --> pdb=" O PHE 2 176 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TRP 2 178 " --> pdb=" O GLY 2 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS 2 36 " --> pdb=" O TRP 2 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 57 through 61 removed outlier: 6.076A pdb=" N GLU 3 57 " --> pdb=" O VAL 3 97 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET 3 99 " --> pdb=" O GLU 3 57 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR 3 59 " --> pdb=" O MET 3 99 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU 3 33 " --> pdb=" O VAL 3 155 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLY 3 157 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE 3 35 " --> pdb=" O GLY 3 157 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE 3 32 " --> pdb=" O GLU 3 174 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE 3 176 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY 3 34 " --> pdb=" O PHE 3 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 57 through 61 removed outlier: 6.441A pdb=" N GLU 4 57 " --> pdb=" O VAL 4 97 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET 4 99 " --> pdb=" O GLU 4 57 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR 4 59 " --> pdb=" O MET 4 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR 4 156 " --> pdb=" O ILE 4 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 57 through 62 removed outlier: 6.385A pdb=" N GLU 5 57 " --> pdb=" O VAL 5 97 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET 5 99 " --> pdb=" O GLU 5 57 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR 5 59 " --> pdb=" O MET 5 99 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN 5 101 " --> pdb=" O THR 5 59 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE 5 61 " --> pdb=" O ASN 5 101 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE 5 154 " --> pdb=" O CYS 5 96 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU 5 98 " --> pdb=" O ILE 5 154 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR 5 156 " --> pdb=" O LEU 5 98 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE 5 100 " --> pdb=" O THR 5 156 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU 5 33 " --> pdb=" O VAL 5 155 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY 5 157 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE 5 35 " --> pdb=" O GLY 5 157 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE 5 32 " --> pdb=" O GLU 5 174 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE 5 176 " --> pdb=" O ILE 5 32 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY 5 34 " --> pdb=" O PHE 5 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '6' and resid 57 through 61 removed outlier: 6.479A pdb=" N GLU 6 57 " --> pdb=" O VAL 6 97 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET 6 99 " --> pdb=" O GLU 6 57 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR 6 59 " --> pdb=" O MET 6 99 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE 6 154 " --> pdb=" O CYS 6 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU 6 98 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR 6 156 " --> pdb=" O LEU 6 98 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE 6 100 " --> pdb=" O THR 6 156 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU 6 33 " --> pdb=" O VAL 6 155 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY 6 157 " --> pdb=" O LEU 6 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE 6 35 " --> pdb=" O GLY 6 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 90 removed outlier: 5.781A pdb=" N CYS A 85 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 103 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 87 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 139 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 40 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY A 309 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 134 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.594A pdb=" N LEU A 170 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN A 402 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 327 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 328 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 266 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS A 295 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS A 268 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HIS A 239 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET A 267 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 241 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP A 269 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 201 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN A 242 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 90 removed outlier: 5.825A pdb=" N CYS B 85 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 103 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 87 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 38 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.259A pdb=" N LEU B 170 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 403 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 172 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 380 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B 328 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 266 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS B 295 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 268 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS B 239 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET B 267 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU B 241 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP B 269 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR B 201 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN B 242 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AB4, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.032A pdb=" N CYS C 85 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA C 103 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 87 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 38 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 139 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 40 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 133 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.321A pdb=" N LEU C 170 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 327 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 292 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N HIS C 328 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N ILE C 294 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 266 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS C 295 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS C 268 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N HIS C 239 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET C 267 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU C 241 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASP C 269 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C 201 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASN C 242 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.031A pdb=" N CYS D 85 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA D 103 " --> pdb=" O CYS D 85 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 87 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 38 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 133 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.326A pdb=" N LEU D 170 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 292 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ILE D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE D 266 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS D 295 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS D 268 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N HIS D 239 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET D 267 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU D 241 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASP D 269 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 201 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN D 242 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 90 removed outlier: 5.780A pdb=" N CYS E 85 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA E 103 " --> pdb=" O CYS E 85 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP E 87 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU E 38 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE E 139 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA E 40 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.438A pdb=" N LEU E 170 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 327 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER E 380 " --> pdb=" O ILE E 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 200 through 202 removed outlier: 7.006A pdb=" N THR E 201 " --> pdb=" O TYR E 240 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN E 242 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N HIS E 239 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET E 267 " --> pdb=" O HIS E 239 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 241 " --> pdb=" O MET E 267 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASP E 269 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 266 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS E 295 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS E 268 " --> pdb=" O HIS E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 90 removed outlier: 5.878A pdb=" N CYS F 85 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA F 103 " --> pdb=" O CYS F 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP F 87 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU F 38 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 133 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.380A pdb=" N LEU F 170 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER F 380 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS F 328 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 266 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N HIS F 295 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS F 268 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS F 239 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET F 267 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 241 " --> pdb=" O MET F 267 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASP F 269 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR F 201 " --> pdb=" O TYR F 240 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN F 242 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AC8, first strand: chain 'G' and resid 84 through 90 removed outlier: 5.897A pdb=" N CYS G 85 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA G 103 " --> pdb=" O CYS G 85 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP G 87 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU G 38 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 139 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA G 40 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA G 133 " --> pdb=" O THR G 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.345A pdb=" N LEU G 170 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE G 327 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER G 380 " --> pdb=" O ILE G 327 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS G 328 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE G 266 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS G 295 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS G 268 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS G 239 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET G 267 " --> pdb=" O HIS G 239 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU G 241 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP G 269 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR G 201 " --> pdb=" O TYR G 240 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ASN G 242 " --> pdb=" O THR G 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AD2, first strand: chain 'H' and resid 84 through 90 removed outlier: 5.840A pdb=" N CYS H 85 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA H 103 " --> pdb=" O CYS H 85 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP H 87 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 38 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 170 through 172 removed outlier: 6.275A pdb=" N LEU H 170 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER H 380 " --> pdb=" O ILE H 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS H 328 " --> pdb=" O ILE H 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE H 266 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS H 295 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS H 268 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N HIS H 239 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET H 267 " --> pdb=" O HIS H 239 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU H 241 " --> pdb=" O MET H 267 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP H 269 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR H 201 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASN H 242 " --> pdb=" O THR H 201 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 354 through 355 Processing sheet with id=AD5, first strand: chain 'I' and resid 54 through 55 removed outlier: 7.342A pdb=" N ILE I 85 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE I 102 " --> pdb=" O ILE I 85 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL I 87 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER I 100 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY I 89 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS I 96 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.704A pdb=" N ILE J 85 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU J 99 " --> pdb=" O GLY J 89 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP J 91 " --> pdb=" O GLN J 97 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN J 97 " --> pdb=" O ASP J 91 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.595A pdb=" N ILE K 85 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU K 99 " --> pdb=" O GLY K 89 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP K 91 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN K 97 " --> pdb=" O ASP K 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.595A pdb=" N ILE L 85 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU L 99 " --> pdb=" O GLY L 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP L 91 " --> pdb=" O GLN L 97 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN L 97 " --> pdb=" O ASP L 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 54 through 55 removed outlier: 7.409A pdb=" N ILE M 85 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE M 102 " --> pdb=" O ILE M 85 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 87 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER M 100 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY M 89 " --> pdb=" O ILE M 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS M 96 " --> pdb=" O ASP M 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.759A pdb=" N ILE N 85 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU N 99 " --> pdb=" O GLY N 89 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP N 91 " --> pdb=" O GLN N 97 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN N 97 " --> pdb=" O ASP N 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 54 through 55 removed outlier: 6.779A pdb=" N ILE O 85 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU O 99 " --> pdb=" O GLY O 89 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP O 91 " --> pdb=" O GLN O 97 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN O 97 " --> pdb=" O ASP O 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 54 through 55 removed outlier: 6.772A pdb=" N ILE P 85 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU P 99 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP P 91 " --> pdb=" O GLN P 97 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN P 97 " --> pdb=" O ASP P 91 " (cutoff:3.500A) 2080 hydrogen bonds defined for protein. 5991 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: 19.97 Time building geometry restraints manager: 14.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 20141 1.40 - 1.57: 30497 1.57 - 1.75: 57 1.75 - 1.93: 271 1.93 - 2.10: 2 Bond restraints: 50968 Sorted by residual: bond pdb=" PG AGS 2 301 " pdb=" S1G AGS 2 301 " ideal model delta sigma weight residual 1.949 1.534 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" PG AGS 5 301 " pdb=" S1G AGS 5 301 " ideal model delta sigma weight residual 1.949 1.672 0.277 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C2 AGS 3 301 " pdb=" N3 AGS 3 301 " ideal model delta sigma weight residual 1.335 1.413 -0.078 1.00e-02 1.00e+04 6.12e+01 bond pdb=" PG AGS 6 301 " pdb=" S1G AGS 6 301 " ideal model delta sigma weight residual 1.949 2.103 -0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" C2 AGS 2 301 " pdb=" N3 AGS 2 301 " ideal model delta sigma weight residual 1.335 1.410 -0.075 1.00e-02 1.00e+04 5.65e+01 ... (remaining 50963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 62263 2.15 - 4.29: 6373 4.29 - 6.44: 508 6.44 - 8.58: 69 8.58 - 10.73: 24 Bond angle restraints: 69237 Sorted by residual: angle pdb=" N1 AGS 5 301 " pdb=" C2 AGS 5 301 " pdb=" N3 AGS 5 301 " ideal model delta sigma weight residual 128.80 118.24 10.56 8.41e-01 1.41e+00 1.58e+02 angle pdb=" N1 AGS 4 301 " pdb=" C2 AGS 4 301 " pdb=" N3 AGS 4 301 " ideal model delta sigma weight residual 128.80 118.32 10.48 8.41e-01 1.41e+00 1.55e+02 angle pdb=" N1 AGS 3 301 " pdb=" C2 AGS 3 301 " pdb=" N3 AGS 3 301 " ideal model delta sigma weight residual 128.80 118.56 10.24 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N1 AGS 2 301 " pdb=" C2 AGS 2 301 " pdb=" N3 AGS 2 301 " ideal model delta sigma weight residual 128.80 118.85 9.95 8.41e-01 1.41e+00 1.40e+02 angle pdb=" N1 AGS 6 301 " pdb=" C2 AGS 6 301 " pdb=" N3 AGS 6 301 " ideal model delta sigma weight residual 128.80 119.08 9.72 8.41e-01 1.41e+00 1.33e+02 ... (remaining 69232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 29602 35.94 - 71.88: 674 71.88 - 107.81: 22 107.81 - 143.75: 11 143.75 - 179.69: 8 Dihedral angle restraints: 30317 sinusoidal: 12338 harmonic: 17979 Sorted by residual: dihedral pdb=" C3 CAP A 502 " pdb=" C CAP A 502 " pdb=" C2 CAP A 502 " pdb=" O6 CAP A 502 " ideal model delta sinusoidal sigma weight residual 81.86 -97.83 179.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -95.94 177.80 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP C 502 " pdb=" C CAP C 502 " pdb=" C2 CAP C 502 " pdb=" O6 CAP C 502 " ideal model delta sinusoidal sigma weight residual 81.86 -101.38 -176.75 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 30314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5759 0.083 - 0.167: 1538 0.167 - 0.250: 238 0.250 - 0.333: 32 0.333 - 0.417: 7 Chirality restraints: 7574 Sorted by residual: chirality pdb=" PB AGS 6 301 " pdb=" O2B AGS 6 301 " pdb=" O3A AGS 6 301 " pdb=" O3B AGS 6 301 " both_signs ideal model delta sigma weight residual True 3.18 -3.60 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" PA AGS 6 301 " pdb=" O2A AGS 6 301 " pdb=" O3A AGS 6 301 " pdb=" O5' AGS 6 301 " both_signs ideal model delta sigma weight residual True 3.18 3.59 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" PA AGS 2 301 " pdb=" O2A AGS 2 301 " pdb=" O3A AGS 2 301 " pdb=" O5' AGS 2 301 " both_signs ideal model delta sigma weight residual True 3.18 3.56 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 7571 not shown) Planarity restraints: 8972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 210 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 211 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 210 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO D 211 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 211 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 211 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 210 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO H 211 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.026 5.00e-02 4.00e+02 ... (remaining 8969 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 12 2.19 - 2.86: 14861 2.86 - 3.54: 63043 3.54 - 4.22: 116232 4.22 - 4.90: 202726 Nonbonded interactions: 396874 Sorted by model distance: nonbonded pdb=" NH1 ARG 6 92 " pdb=" OE1 GLU A 52 " model vdw 1.507 3.120 nonbonded pdb=" CD2 TYR 2 143 " pdb=" SD MET P 1 " model vdw 1.675 3.700 nonbonded pdb=" O2G AGS 5 301 " pdb="MG MG 5 302 " model vdw 1.828 2.170 nonbonded pdb=" O2G AGS 2 301 " pdb="MG MG 2 302 " model vdw 1.856 2.170 nonbonded pdb=" O2G AGS 4 301 " pdb="MG MG 4 302 " model vdw 1.916 2.170 ... (remaining 396869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 2 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 248 or resid 253 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 \ through 281)) selection = (chain '2' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 114 or (resid 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 through 200 or (resid 201 a \ nd (name N or name CA or name C or name O or name CB )) or resid 202 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 239 or (resid 240 and (name N or name CA or name C or name O or nam \ e CB )) or resid 241 through 248 or resid 253 through 254 or (resid 255 and (nam \ e N or name CA or name C or name O or name CB )) or resid 256 or (resid 257 thro \ ugh 258 and (name N or name CA or name C or name O or name CB )) or resid 259 th \ rough 281)) selection = (chain '3' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 194 \ or (resid 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB )) or resid 213 through 239 or (resid 240 and (name N or na \ me CA or name C or name O or name CB )) or resid 241 through 248 or resid 253 th \ rough 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 through 280 or (resid 281 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain '4' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 194 \ or (resid 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB )) or resid 213 through 239 or (resid 240 and (name N or na \ me CA or name C or name O or name CB )) or resid 241 through 248 or resid 253 th \ rough 256 or (resid 257 through 258 and (name N or name CA or name C or name O o \ r name CB )) or resid 259 through 281)) selection = (chain '5' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 200 \ or (resid 201 and (name N or name CA or name C or name O or name CB )) or resid \ 202 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB )) or resid 241 through 248 or resid 253 through 256 or (re \ sid 257 through 258 and (name N or name CA or name C or name O or name CB )) or \ resid 259 through 281)) selection = (chain '6' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 200 \ or (resid 201 and (name N or name CA or name C or name O or name CB )) or resid \ 202 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB )) or resid 241 through 281)) } ncs_group { reference = (chain 'A' and (resid 3 or resid 9 or resid 24 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 338 or (resi \ d 339 and (name N or name CA or name C or name O or name CB )) or resid 340 thro \ ugh 468 or (resid 469 and (name N or name CA or name C or name O or name CB )) o \ r resid 470 or (resid 471 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 14 or resid 19 or resid 24 through 471)) selection = (chain 'C' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.130 Check model and map are aligned: 0.360 Set scattering table: 0.420 Process input model: 108.570 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.270 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.008 0.415 50968 Z= 0.561 Angle : 1.333 10.728 69237 Z= 0.897 Chirality : 0.075 0.417 7574 Planarity : 0.004 0.057 8972 Dihedral : 15.600 179.689 18805 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 1.00 % Allowed : 5.36 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: -1.92 (0.09), residues: 6183 helix: -1.42 (0.08), residues: 2506 sheet: 0.20 (0.16), residues: 909 loop : -1.54 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 53 HIS 0.007 0.001 HIS 1 265 PHE 0.017 0.002 PHE A 346 TYR 0.015 0.002 TYR H 240 ARG 0.005 0.000 ARG 1 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 1408 time to evaluate : 5.776 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: 1 62 SER cc_start: 0.7517 (t) cc_final: 0.7228 (p) REVERT: 1 76 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7673 (ttt180) REVERT: 1 87 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7440 (mt-10) REVERT: 1 149 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7527 (tpp80) REVERT: 2 128 MET cc_start: 0.6456 (mtm) cc_final: 0.6186 (mtp) REVERT: 3 257 LYS cc_start: 0.7178 (pttt) cc_final: 0.6175 (tppt) REVERT: 3 282 ASN cc_start: 0.4863 (m-40) cc_final: 0.4268 (p0) REVERT: 4 51 PHE cc_start: 0.4914 (m-10) cc_final: 0.4584 (m-80) REVERT: 4 213 GLN cc_start: 0.3918 (mm-40) cc_final: 0.3639 (mm110) REVERT: 4 258 LYS cc_start: 0.5231 (mmtt) cc_final: 0.4863 (tmmt) REVERT: 6 104 ASP cc_start: 0.6664 (t0) cc_final: 0.6413 (p0) REVERT: 6 164 TYR cc_start: 0.7382 (t80) cc_final: 0.6962 (t80) REVERT: 6 206 LEU cc_start: 0.7079 (tp) cc_final: 0.6753 (tt) REVERT: B 15 LYS cc_start: 0.7877 (tttt) cc_final: 0.7658 (ttpp) REVERT: C 27 THR cc_start: 0.8435 (p) cc_final: 0.8230 (t) REVERT: C 437 ASN cc_start: 0.7462 (t0) cc_final: 0.7114 (t0) REVERT: D 467 LYS cc_start: 0.8447 (tptt) cc_final: 0.8085 (mttp) REVERT: E 89 GLU cc_start: 0.7619 (tt0) cc_final: 0.7213 (tm-30) REVERT: E 437 ASN cc_start: 0.7382 (t0) cc_final: 0.7140 (t0) REVERT: E 447 ARG cc_start: 0.7412 (ttm110) cc_final: 0.7161 (mtm-85) REVERT: E 475 THR cc_start: 0.4942 (OUTLIER) cc_final: 0.4601 (p) REVERT: E 476 VAL cc_start: 0.2392 (OUTLIER) cc_final: 0.2109 (t) REVERT: F 47 PRO cc_start: 0.7604 (Cg_exo) cc_final: 0.7035 (Cg_endo) REVERT: F 73 ASP cc_start: 0.6722 (m-30) cc_final: 0.6470 (p0) REVERT: F 397 ASP cc_start: 0.7500 (m-30) cc_final: 0.7294 (m-30) REVERT: F 464 LYS cc_start: 0.7305 (tptt) cc_final: 0.6485 (ttmt) REVERT: F 466 ILE cc_start: 0.8015 (mm) cc_final: 0.7749 (mp) REVERT: F 475 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5389 (p) REVERT: F 476 VAL cc_start: 0.4647 (OUTLIER) cc_final: 0.4332 (m) REVERT: G 15 LYS cc_start: 0.8561 (tttt) cc_final: 0.8114 (mtmt) REVERT: G 22 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7378 (tpt90) REVERT: G 248 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6877 (m) REVERT: G 361 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7406 (mtt90) REVERT: G 443 ASN cc_start: 0.8033 (m110) cc_final: 0.7730 (m-40) REVERT: G 469 GLU cc_start: 0.6264 (mt-10) cc_final: 0.6018 (mp0) REVERT: G 475 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5140 (m) REVERT: H 81 TYR cc_start: 0.8787 (m-80) cc_final: 0.8476 (m-80) REVERT: H 303 ASP cc_start: 0.7740 (p0) cc_final: 0.7465 (t0) REVERT: H 441 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6874 (mp0) REVERT: I 57 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7877 (mtpt) REVERT: I 72 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7838 (mm-30) REVERT: J 6 LYS cc_start: 0.8584 (mttt) cc_final: 0.8269 (mmtp) REVERT: J 93 ILE cc_start: 0.7946 (mt) cc_final: 0.7521 (mt) REVERT: J 94 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8217 (mtmt) REVERT: O 65 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7279 (m) REVERT: P 7 GLU cc_start: 0.6782 (tt0) cc_final: 0.6162 (pm20) REVERT: P 79 GLN cc_start: 0.8552 (tp40) cc_final: 0.8270 (tp40) REVERT: P 93 ILE cc_start: 0.8847 (mt) cc_final: 0.8641 (mm) outliers start: 52 outliers final: 11 residues processed: 1448 average time/residue: 1.7635 time to fit residues: 3131.0403 Evaluate side-chains 627 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 609 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 ASN Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 6 residue 183 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 248 CYS Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain O residue 65 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 518 optimal weight: 0.9980 chunk 465 optimal weight: 10.0000 chunk 258 optimal weight: 0.0370 chunk 158 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 481 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 557 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 158 ASN 1 248 ASN 1 265 HIS 2 158 ASN 2 271 ASN 3 158 ASN ** 4 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 119 ASN 4 133 ASN 4 158 ASN 4 265 HIS 5 16 HIS 5 46 GLN ** 5 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** 6 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 129 ASN 6 146 ASN A 116 ASN A 154 HIS A 326 HIS B 96 ASN B 154 HIS B 213 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS C 213 GLN D 46 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS D 213 GLN E 154 HIS ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 154 HIS F 437 ASN G 97 GLN G 116 ASN G 154 HIS G 213 GLN H 154 HIS H 213 GLN H 443 ASN I 27 GLN K 95 GLN L 97 GLN M 2 GLN M 97 GLN N 79 GLN O 97 GLN P 95 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 50968 Z= 0.225 Angle : 0.626 7.564 69237 Z= 0.331 Chirality : 0.044 0.202 7574 Planarity : 0.005 0.065 8972 Dihedral : 9.576 179.431 7120 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.13 % Allowed : 15.77 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: -0.21 (0.10), residues: 6183 helix: 0.79 (0.09), residues: 2591 sheet: 0.28 (0.17), residues: 870 loop : -1.18 (0.10), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 215 HIS 0.009 0.001 HIS 6 36 PHE 0.034 0.002 PHE A 346 TYR 0.018 0.001 TYR 6 177 ARG 0.009 0.001 ARG 4 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 662 time to evaluate : 5.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 62 SER cc_start: 0.7402 (t) cc_final: 0.7154 (p) REVERT: 1 87 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7491 (mt-10) REVERT: 1 149 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7589 (mtt-85) REVERT: 2 258 LYS cc_start: 0.4982 (OUTLIER) cc_final: 0.4667 (tptt) REVERT: 4 38 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.4288 (mmp80) REVERT: 4 133 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6544 (p0) REVERT: 4 136 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.5483 (t0) REVERT: 6 73 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: 6 81 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7460 (mtt-85) REVERT: 6 226 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.6181 (t80) REVERT: 6 233 PHE cc_start: 0.7499 (t80) cc_final: 0.6968 (t80) REVERT: A 453 SER cc_start: 0.8473 (t) cc_final: 0.8183 (t) REVERT: B 15 LYS cc_start: 0.7808 (tttt) cc_final: 0.7525 (ttpp) REVERT: B 303 ASP cc_start: 0.7438 (p0) cc_final: 0.7120 (t0) REVERT: B 466 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.7980 (pp) REVERT: C 90 PRO cc_start: 0.7876 (Cg_endo) cc_final: 0.7638 (Cg_exo) REVERT: C 437 ASN cc_start: 0.7741 (t0) cc_final: 0.7490 (t0) REVERT: D 467 LYS cc_start: 0.8362 (tptt) cc_final: 0.8116 (mttp) REVERT: E 89 GLU cc_start: 0.7746 (tt0) cc_final: 0.7173 (tm-30) REVERT: E 447 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7057 (mtm-85) REVERT: E 475 THR cc_start: 0.5311 (OUTLIER) cc_final: 0.5045 (p) REVERT: F 47 PRO cc_start: 0.7639 (Cg_exo) cc_final: 0.7160 (Cg_endo) REVERT: F 73 ASP cc_start: 0.6670 (m-30) cc_final: 0.6431 (p0) REVERT: F 344 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7468 (mpm) REVERT: F 475 THR cc_start: 0.5818 (OUTLIER) cc_final: 0.5428 (p) REVERT: F 476 VAL cc_start: 0.4438 (OUTLIER) cc_final: 0.3964 (t) REVERT: G 15 LYS cc_start: 0.8598 (tttt) cc_final: 0.8137 (mtpt) REVERT: G 22 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7516 (tpt90) REVERT: G 128 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: G 157 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: G 249 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: G 361 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7481 (mtt180) REVERT: G 444 ASP cc_start: 0.7741 (t0) cc_final: 0.7538 (t0) REVERT: G 467 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6169 (mttp) REVERT: G 469 GLU cc_start: 0.6132 (mt-10) cc_final: 0.5930 (mp0) REVERT: H 53 GLU cc_start: 0.7368 (tp30) cc_final: 0.7160 (tm-30) REVERT: H 157 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7518 (mm-40) REVERT: H 303 ASP cc_start: 0.7722 (p0) cc_final: 0.7482 (t0) REVERT: H 441 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6901 (mp0) REVERT: I 86 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8273 (ptt180) REVERT: J 2 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: J 25 GLU cc_start: 0.7590 (tp30) cc_final: 0.6936 (tp30) REVERT: J 93 ILE cc_start: 0.7831 (mt) cc_final: 0.7580 (mt) REVERT: J 94 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8317 (mtmt) REVERT: L 21 ASP cc_start: 0.7713 (m-30) cc_final: 0.7497 (m-30) REVERT: M 79 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: N 51 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8494 (pp) REVERT: N 57 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8154 (mttt) REVERT: O 65 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6884 (m) REVERT: P 79 GLN cc_start: 0.8450 (tp40) cc_final: 0.8167 (tp40) outliers start: 215 outliers final: 58 residues processed: 827 average time/residue: 1.6747 time to fit residues: 1724.4547 Evaluate side-chains 620 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 539 time to evaluate : 5.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 48 GLU Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 115 GLN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 230 ILE Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 60 LEU Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 133 ASN Chi-restraints excluded: chain 4 residue 136 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 157 GLN Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 309 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 464 optimal weight: 7.9990 chunk 379 optimal weight: 0.4980 chunk 153 optimal weight: 8.9990 chunk 558 optimal weight: 0.8980 chunk 603 optimal weight: 1.9990 chunk 497 optimal weight: 0.4980 chunk 553 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 448 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 GLN 1 205 GLN 1 248 ASN 2 115 GLN ** 2 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 115 GLN 4 121 GLN 4 133 ASN 4 213 GLN ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 46 GLN 5 200 GLN 6 20 ASN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 414 ASN G 97 GLN I 27 GLN K 95 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 50968 Z= 0.156 Angle : 0.532 10.714 69237 Z= 0.277 Chirality : 0.041 0.171 7574 Planarity : 0.004 0.059 8972 Dihedral : 8.779 178.380 7105 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.69 % Allowed : 17.92 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.47 (0.10), residues: 6183 helix: 1.54 (0.10), residues: 2572 sheet: 0.66 (0.17), residues: 853 loop : -1.01 (0.10), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.013 0.001 HIS 1 235 PHE 0.031 0.002 PHE A 346 TYR 0.017 0.001 TYR 1 226 ARG 0.008 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 613 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: 1 62 SER cc_start: 0.7299 (t) cc_final: 0.7037 (p) REVERT: 1 87 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7473 (mt-10) REVERT: 1 149 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7525 (mtt-85) REVERT: 1 205 GLN cc_start: 0.6893 (tp40) cc_final: 0.6643 (tp-100) REVERT: 1 245 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.3234 (ptm-80) REVERT: 2 258 LYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4667 (tptm) REVERT: 3 213 GLN cc_start: 0.5299 (mm-40) cc_final: 0.5015 (mm110) REVERT: 3 236 LYS cc_start: 0.6539 (pptt) cc_final: 0.5993 (mmpt) REVERT: 3 267 ILE cc_start: 0.5197 (mp) cc_final: 0.4973 (tp) REVERT: 4 38 ARG cc_start: 0.4941 (OUTLIER) cc_final: 0.4124 (mmp80) REVERT: 4 150 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5358 (ttt180) REVERT: 6 73 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: 6 81 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7380 (mtt-85) REVERT: 6 226 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.6154 (t80) REVERT: 6 233 PHE cc_start: 0.7652 (t80) cc_final: 0.7179 (t80) REVERT: A 453 SER cc_start: 0.8192 (t) cc_final: 0.7863 (t) REVERT: B 15 LYS cc_start: 0.7843 (tttt) cc_final: 0.7604 (ttpp) REVERT: C 27 THR cc_start: 0.8696 (p) cc_final: 0.8462 (t) REVERT: C 90 PRO cc_start: 0.7867 (Cg_endo) cc_final: 0.7641 (Cg_exo) REVERT: C 437 ASN cc_start: 0.7891 (t0) cc_final: 0.7588 (t0) REVERT: C 448 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: D 120 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 352 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8079 (mm-30) REVERT: D 444 ASP cc_start: 0.7718 (t0) cc_final: 0.7504 (t0) REVERT: D 467 LYS cc_start: 0.8420 (tptt) cc_final: 0.8145 (mttp) REVERT: E 89 GLU cc_start: 0.7749 (tt0) cc_final: 0.7226 (tm-30) REVERT: E 447 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7125 (mtm-85) REVERT: E 475 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.4828 (p) REVERT: F 47 PRO cc_start: 0.7736 (Cg_exo) cc_final: 0.7285 (Cg_endo) REVERT: F 344 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7535 (mpm) REVERT: F 475 THR cc_start: 0.5892 (OUTLIER) cc_final: 0.5567 (p) REVERT: G 15 LYS cc_start: 0.8562 (tttt) cc_final: 0.8084 (mtpt) REVERT: G 22 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7369 (tpt90) REVERT: G 128 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: G 467 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6278 (mttp) REVERT: G 469 GLU cc_start: 0.6160 (mt-10) cc_final: 0.5931 (mp0) REVERT: H 441 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6891 (mp0) REVERT: I 72 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8199 (mm-30) REVERT: J 94 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8332 (mtmt) REVERT: K 20 THR cc_start: 0.6731 (OUTLIER) cc_final: 0.6474 (p) REVERT: L 20 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6605 (p) REVERT: L 21 ASP cc_start: 0.7758 (m-30) cc_final: 0.7423 (m-30) REVERT: N 51 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8489 (pp) REVERT: N 57 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7920 (mtmt) REVERT: O 34 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7594 (mm110) REVERT: O 57 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8008 (mtpt) REVERT: P 2 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6633 (mt0) REVERT: P 51 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8326 (pp) outliers start: 192 outliers final: 62 residues processed: 755 average time/residue: 1.6732 time to fit residues: 1570.3176 Evaluate side-chains 594 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 510 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 57 GLU Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 225 ILE Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 1 residue 245 ARG Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 192 ILE Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 2 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 60 LEU Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 551 optimal weight: 2.9990 chunk 419 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 266 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 chunk 560 optimal weight: 8.9990 chunk 593 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 531 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 16 HIS 1 121 GLN 1 200 GLN ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 36 HIS 3 229 GLN ** 4 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 213 GLN ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 46 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 248 ASN B 208 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 185 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN G 97 GLN G 116 ASN G 208 ASN I 27 GLN I 97 GLN K 74 GLN K 95 GLN L 95 GLN P 97 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 50968 Z= 0.343 Angle : 0.659 8.817 69237 Z= 0.343 Chirality : 0.047 0.201 7574 Planarity : 0.005 0.061 8972 Dihedral : 8.785 176.791 7103 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.98 % Allowed : 17.69 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.26 (0.10), residues: 6183 helix: 1.44 (0.10), residues: 2570 sheet: 0.84 (0.18), residues: 697 loop : -1.19 (0.10), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 215 HIS 0.016 0.002 HIS 6 235 PHE 0.032 0.002 PHE B 346 TYR 0.023 0.002 TYR 6 164 ARG 0.007 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 560 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 57 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: 1 149 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7414 (mtt-85) REVERT: 2 258 LYS cc_start: 0.5167 (OUTLIER) cc_final: 0.4765 (tptm) REVERT: 3 12 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.5286 (mmtm) REVERT: 3 213 GLN cc_start: 0.5429 (mm-40) cc_final: 0.5113 (mm-40) REVERT: 3 236 LYS cc_start: 0.6423 (pptt) cc_final: 0.5887 (mmpt) REVERT: 3 257 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5837 (pmtt) REVERT: 3 271 ASN cc_start: 0.4837 (OUTLIER) cc_final: 0.4636 (t0) REVERT: 4 38 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.4091 (mmp80) REVERT: 4 136 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5415 (p0) REVERT: 4 235 HIS cc_start: 0.6314 (OUTLIER) cc_final: 0.5938 (t70) REVERT: 5 279 ARG cc_start: 0.6176 (tpp-160) cc_final: 0.5607 (tmm160) REVERT: 6 73 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: 6 87 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: 6 226 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6179 (t80) REVERT: 6 233 PHE cc_start: 0.7896 (t80) cc_final: 0.7676 (t80) REVERT: A 89 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: A 441 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: B 15 LYS cc_start: 0.7977 (tttt) cc_final: 0.7713 (ttpp) REVERT: C 90 PRO cc_start: 0.8128 (Cg_endo) cc_final: 0.7891 (Cg_exo) REVERT: C 437 ASN cc_start: 0.8116 (t0) cc_final: 0.7772 (t0) REVERT: C 448 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: D 444 ASP cc_start: 0.7730 (t0) cc_final: 0.7426 (t0) REVERT: E 89 GLU cc_start: 0.7922 (tt0) cc_final: 0.7385 (tm-30) REVERT: E 475 THR cc_start: 0.5709 (OUTLIER) cc_final: 0.5448 (p) REVERT: F 19 GLN cc_start: 0.7344 (tt0) cc_final: 0.6912 (tt0) REVERT: F 132 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7737 (ptm160) REVERT: F 344 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7745 (mpm) REVERT: F 451 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7887 (pttp) REVERT: G 15 LYS cc_start: 0.8494 (tttt) cc_final: 0.8015 (mtpt) REVERT: G 22 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7410 (tpt90) REVERT: G 356 GLU cc_start: 0.7418 (tp30) cc_final: 0.7040 (tt0) REVERT: G 467 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6357 (mttp) REVERT: G 469 GLU cc_start: 0.6172 (mt-10) cc_final: 0.5935 (mp0) REVERT: H 15 LYS cc_start: 0.7578 (tttt) cc_final: 0.7376 (mmtt) REVERT: H 157 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: H 441 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6785 (mp0) REVERT: I 72 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8287 (tp30) REVERT: J 2 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: J 25 GLU cc_start: 0.7758 (tp30) cc_final: 0.7283 (tp30) REVERT: J 94 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8410 (mtmt) REVERT: K 51 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8409 (pp) REVERT: L 20 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.6819 (p) REVERT: L 21 ASP cc_start: 0.7902 (m-30) cc_final: 0.7648 (m-30) REVERT: L 49 THR cc_start: 0.8619 (m) cc_final: 0.8354 (p) REVERT: M 79 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: M 92 ASN cc_start: 0.7610 (t0) cc_final: 0.7260 (t0) REVERT: N 51 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8588 (pp) REVERT: O 34 GLN cc_start: 0.8109 (mp10) cc_final: 0.7815 (mm110) REVERT: P 2 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6884 (mt0) REVERT: P 51 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8469 (pp) outliers start: 259 outliers final: 100 residues processed: 757 average time/residue: 1.7036 time to fit residues: 1600.7952 Evaluate side-chains 605 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 480 time to evaluate : 5.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 57 GLU Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 214 SER Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 228 ILE Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 192 ILE Chi-restraints excluded: chain 3 residue 199 SER Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 3 residue 271 ASN Chi-restraints excluded: chain 4 residue 2 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 60 LEU Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 99 MET Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 136 ASP Chi-restraints excluded: chain 4 residue 153 ILE Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 494 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 441 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 506 optimal weight: 5.9990 chunk 410 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 532 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 200 GLN ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 23 ASN ** 4 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 213 GLN 5 46 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 248 ASN 6 265 HIS B 157 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN I 27 GLN I 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 50968 Z= 0.326 Angle : 0.622 13.578 69237 Z= 0.323 Chirality : 0.045 0.196 7574 Planarity : 0.005 0.060 8972 Dihedral : 8.644 176.723 7100 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.69 % Allowed : 19.30 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.27 (0.10), residues: 6183 helix: 1.46 (0.10), residues: 2571 sheet: 0.79 (0.17), residues: 751 loop : -1.22 (0.10), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 178 HIS 0.012 0.001 HIS 5 16 PHE 0.034 0.002 PHE B 346 TYR 0.021 0.002 TYR 1 4 ARG 0.013 0.001 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 505 time to evaluate : 5.932 Fit side-chains revert: symmetry clash REVERT: 1 45 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.5924 (t80) REVERT: 1 149 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7412 (mtt-85) REVERT: 1 185 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6855 (pttt) REVERT: 2 133 ASN cc_start: 0.7778 (m110) cc_final: 0.7512 (m-40) REVERT: 2 138 GLN cc_start: 0.7831 (pt0) cc_final: 0.7558 (pm20) REVERT: 2 258 LYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4674 (tptm) REVERT: 3 12 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5193 (mmtm) REVERT: 3 204 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6164 (mt-10) REVERT: 3 213 GLN cc_start: 0.5606 (mm-40) cc_final: 0.5249 (mm-40) REVERT: 3 236 LYS cc_start: 0.6446 (pptt) cc_final: 0.5911 (mmpt) REVERT: 3 257 LYS cc_start: 0.6038 (OUTLIER) cc_final: 0.5682 (pmtt) REVERT: 3 267 ILE cc_start: 0.5152 (mp) cc_final: 0.4851 (tp) REVERT: 4 38 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.4065 (mmp80) REVERT: 4 136 ASP cc_start: 0.5689 (OUTLIER) cc_final: 0.5375 (p0) REVERT: 4 150 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5182 (ttt180) REVERT: 4 235 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5937 (t70) REVERT: 5 229 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: 5 279 ARG cc_start: 0.6278 (tpp-160) cc_final: 0.5715 (tmm160) REVERT: 6 5 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7824 (tp) REVERT: 6 38 ARG cc_start: 0.6804 (ttp80) cc_final: 0.6596 (ttp80) REVERT: 6 73 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: 6 87 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: 6 226 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6533 (t80) REVERT: A 89 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: B 15 LYS cc_start: 0.8021 (tttt) cc_final: 0.7711 (ttpp) REVERT: B 140 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.6702 (tmm160) REVERT: C 90 PRO cc_start: 0.8159 (Cg_endo) cc_final: 0.7911 (Cg_exo) REVERT: C 437 ASN cc_start: 0.8108 (t0) cc_final: 0.7775 (t0) REVERT: C 448 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: D 120 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8445 (m) REVERT: D 434 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 444 ASP cc_start: 0.7755 (t0) cc_final: 0.7397 (t0) REVERT: E 89 GLU cc_start: 0.8014 (tt0) cc_final: 0.7476 (tm-30) REVERT: E 475 THR cc_start: 0.5558 (OUTLIER) cc_final: 0.5158 (p) REVERT: F 132 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7712 (ptm160) REVERT: F 344 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7675 (mpm) REVERT: F 451 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7856 (pttp) REVERT: F 475 THR cc_start: 0.6119 (OUTLIER) cc_final: 0.5872 (p) REVERT: G 15 LYS cc_start: 0.8510 (tttt) cc_final: 0.8043 (mtpt) REVERT: G 119 THR cc_start: 0.9165 (m) cc_final: 0.8961 (m) REVERT: G 249 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: G 467 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6245 (mttp) REVERT: G 469 GLU cc_start: 0.6208 (mt-10) cc_final: 0.5879 (mp0) REVERT: H 157 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: H 250 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: H 303 ASP cc_start: 0.8192 (p0) cc_final: 0.7604 (t0) REVERT: H 441 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6870 (mp0) REVERT: I 72 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8365 (tp30) REVERT: J 24 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8329 (mm) REVERT: J 29 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8410 (tp-100) REVERT: J 94 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8397 (mtmt) REVERT: K 51 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8495 (pp) REVERT: L 20 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6884 (p) REVERT: L 49 THR cc_start: 0.8650 (m) cc_final: 0.8310 (p) REVERT: M 79 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: N 51 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8595 (pp) REVERT: O 34 GLN cc_start: 0.8135 (mp10) cc_final: 0.7905 (mm110) REVERT: P 2 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6948 (mt0) REVERT: P 51 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (pp) outliers start: 244 outliers final: 93 residues processed: 687 average time/residue: 1.7880 time to fit residues: 1514.7337 Evaluate side-chains 583 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 459 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 45 PHE Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 214 SER Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 244 LEU Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 144 ASP Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 199 SER Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 136 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 229 GLN Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 199 optimal weight: 9.9990 chunk 534 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 594 optimal weight: 7.9990 chunk 493 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 36 HIS 1 200 GLN ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 213 GLN 5 46 GLN ** 5 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 229 GLN 6 265 HIS A 157 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN D 19 GLN D 208 ASN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 357 GLN G 97 GLN G 278 ASN G 387 HIS I 97 GLN P 104 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 50968 Z= 0.453 Angle : 0.699 11.645 69237 Z= 0.363 Chirality : 0.049 0.217 7574 Planarity : 0.006 0.058 8972 Dihedral : 8.676 177.150 7100 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.92 % Allowed : 19.55 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: -0.03 (0.10), residues: 6183 helix: 1.18 (0.10), residues: 2589 sheet: 0.33 (0.17), residues: 788 loop : -1.30 (0.10), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 4 178 HIS 0.014 0.002 HIS 5 16 PHE 0.033 0.002 PHE B 346 TYR 0.025 0.002 TYR 2 116 ARG 0.009 0.001 ARG 4 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 491 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.6335 (t80) REVERT: 1 57 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7393 (mt-10) REVERT: 1 84 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7707 (mm-30) REVERT: 1 149 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7296 (mtp-110) REVERT: 2 10 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7712 (tt) REVERT: 2 19 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7683 (mtmt) REVERT: 2 54 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: 2 138 GLN cc_start: 0.8052 (pt0) cc_final: 0.7679 (pm20) REVERT: 2 241 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4121 (ppp80) REVERT: 2 257 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6280 (ttmm) REVERT: 2 258 LYS cc_start: 0.5164 (OUTLIER) cc_final: 0.4727 (tptt) REVERT: 3 12 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.5277 (mmtm) REVERT: 3 213 GLN cc_start: 0.5909 (mm-40) cc_final: 0.5514 (mm-40) REVERT: 3 236 LYS cc_start: 0.6420 (pptt) cc_final: 0.5858 (mmpt) REVERT: 3 257 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5760 (pmtt) REVERT: 3 267 ILE cc_start: 0.5129 (mp) cc_final: 0.4800 (tp) REVERT: 3 271 ASN cc_start: 0.4903 (OUTLIER) cc_final: 0.4695 (t0) REVERT: 4 38 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.3859 (mmp80) REVERT: 4 136 ASP cc_start: 0.5500 (OUTLIER) cc_final: 0.5209 (p0) REVERT: 4 150 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.5451 (ttt180) REVERT: 4 198 LEU cc_start: 0.1953 (OUTLIER) cc_final: 0.1430 (tp) REVERT: 4 235 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.5946 (t70) REVERT: 5 16 HIS cc_start: 0.7236 (t70) cc_final: 0.6918 (t70) REVERT: 5 128 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7093 (ttp) REVERT: 5 173 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5570 (tmm) REVERT: 5 229 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: 5 279 ARG cc_start: 0.6203 (tpp-160) cc_final: 0.5700 (tmm160) REVERT: 6 73 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: 6 87 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: 6 109 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5411 (mtt90) REVERT: 6 226 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6464 (t80) REVERT: A 89 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: B 140 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.6903 (tmm160) REVERT: C 90 PRO cc_start: 0.8210 (Cg_endo) cc_final: 0.7977 (Cg_exo) REVERT: C 448 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: D 120 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8500 (m) REVERT: D 337 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: D 434 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 444 ASP cc_start: 0.7753 (t0) cc_final: 0.7381 (t0) REVERT: E 15 LYS cc_start: 0.8632 (tttt) cc_final: 0.7962 (tptp) REVERT: E 89 GLU cc_start: 0.8032 (tt0) cc_final: 0.7469 (tm-30) REVERT: E 475 THR cc_start: 0.5622 (OUTLIER) cc_final: 0.5341 (p) REVERT: F 344 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7706 (mpm) REVERT: F 451 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7880 (pttp) REVERT: G 15 LYS cc_start: 0.8458 (tttt) cc_final: 0.8004 (mtpt) REVERT: G 467 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6389 (mttp) REVERT: H 157 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7591 (mm-40) REVERT: H 250 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: H 303 ASP cc_start: 0.8276 (p0) cc_final: 0.7672 (t0) REVERT: H 441 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6750 (mp0) REVERT: I 72 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8406 (tp30) REVERT: J 2 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: J 29 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8465 (tp-100) REVERT: J 94 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8411 (mtmt) REVERT: K 44 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: K 105 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8356 (mtpt) REVERT: L 11 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7638 (mt-10) REVERT: L 20 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7107 (p) REVERT: L 49 THR cc_start: 0.8667 (m) cc_final: 0.8270 (p) REVERT: L 91 ASP cc_start: 0.8341 (t0) cc_final: 0.8103 (t0) REVERT: M 79 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: N 51 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8668 (pp) REVERT: O 34 GLN cc_start: 0.8206 (mp10) cc_final: 0.7993 (mm110) REVERT: P 2 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7142 (mt0) outliers start: 256 outliers final: 117 residues processed: 693 average time/residue: 1.7984 time to fit residues: 1533.4189 Evaluate side-chains 609 residues out of total 5254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 454 time to evaluate : 5.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 45 PHE Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 122 LEU Chi-restraints excluded: chain 1 residue 126 THR Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 214 SER Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 228 ILE Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 54 MET Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 173 MET Chi-restraints excluded: chain 2 residue 221 LEU Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 244 LEU Chi-restraints excluded: chain 2 residue 257 LYS Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 144 ASP Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 168 ILE Chi-restraints excluded: chain 3 residue 189 VAL Chi-restraints excluded: chain 3 residue 199 SER Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 3 residue 271 ASN Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 99 MET Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 136 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 128 MET Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 173 MET Chi-restraints excluded: chain 5 residue 229 GLN Chi-restraints excluded: chain 6 residue 48 GLU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 109 ARG Chi-restraints excluded: chain 6 residue 124 ASN Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0056 > 50: distance: 44 - 167: 16.675 distance: 57 - 151: 15.025 distance: 60 - 148: 5.621 distance: 72 - 138: 13.514 distance: 75 - 135: 8.685 distance: 119 - 124: 5.605 distance: 125 - 126: 3.727 distance: 125 - 128: 5.990 distance: 126 - 127: 3.604 distance: 126 - 135: 3.500 distance: 128 - 129: 4.222 distance: 129 - 130: 10.553 distance: 130 - 131: 5.552 distance: 132 - 133: 10.121 distance: 132 - 134: 3.158 distance: 135 - 136: 7.999 distance: 136 - 139: 11.164 distance: 137 - 138: 3.202 distance: 140 - 141: 5.059 distance: 141 - 142: 3.342 distance: 141 - 144: 3.623 distance: 142 - 143: 4.256 distance: 143 - 257: 6.506 distance: 145 - 146: 3.811 distance: 145 - 147: 6.130 distance: 148 - 149: 7.484 distance: 149 - 150: 4.230 distance: 149 - 152: 6.956 distance: 150 - 151: 3.011 distance: 152 - 153: 5.845 distance: 153 - 154: 5.889 distance: 156 - 158: 3.474 distance: 159 - 160: 6.985 distance: 159 - 260: 11.445 distance: 160 - 161: 6.667 distance: 160 - 163: 5.224 distance: 161 - 162: 5.621 distance: 161 - 167: 8.353 distance: 164 - 165: 3.945 distance: 164 - 166: 7.810 distance: 167 - 168: 5.321 distance: 168 - 169: 4.045 distance: 168 - 171: 6.115 distance: 169 - 170: 12.878 distance: 169 - 176: 9.580 distance: 171 - 172: 5.794 distance: 172 - 173: 6.545 distance: 173 - 175: 6.927 distance: 176 - 177: 6.809 distance: 177 - 178: 10.872 distance: 177 - 180: 11.305 distance: 178 - 179: 16.160 distance: 178 - 184: 23.778 distance: 180 - 181: 7.153 distance: 181 - 182: 11.802 distance: 181 - 183: 3.155 distance: 184 - 185: 22.513 distance: 185 - 186: 10.898 distance: 185 - 188: 19.632 distance: 186 - 187: 11.109 distance: 186 - 192: 18.030 distance: 188 - 189: 22.788 distance: 188 - 190: 34.126 distance: 189 - 191: 26.438 distance: 192 - 193: 11.244 distance: 193 - 194: 18.998 distance: 193 - 196: 14.463 distance: 194 - 195: 16.153 distance: 194 - 203: 18.787 distance: 196 - 197: 15.732 distance: 197 - 198: 13.291 distance: 198 - 199: 8.424 distance: 199 - 200: 15.412 distance: 200 - 201: 15.454 distance: 200 - 202: 17.678 distance: 203 - 204: 8.458 distance: 204 - 205: 7.020 distance: 204 - 207: 11.215 distance: 205 - 206: 21.671 distance: 205 - 214: 8.755 distance: 207 - 208: 13.488 distance: 208 - 209: 12.559 distance: 208 - 210: 14.693 distance: 209 - 211: 9.320 distance: 210 - 212: 10.336 distance: 211 - 213: 4.783 distance: 212 - 213: 21.367