Starting phenix.real_space_refine on Sun Mar 24 17:49:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jak_6349/03_2024/3jak_6349_updated.pdb" } resolution = 3.3 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= 0.028 sd= 0.918 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 36 5.49 5 Mg 6 5.21 5 S 296 5.16 5 C 27084 2.51 5 N 7340 2.21 5 O 8304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "M PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43066 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3385 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.35, per 1000 atoms: 0.52 Number of scatterers: 43066 At special positions: 0 Unit cell: (171.6, 113.52, 212.52, 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 296 16.00 P 36 15.00 Mg 6 11.99 O 8304 8.00 N 7340 7.00 C 27084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.86 Conformation dependent library (CDL) restraints added in 7.9 seconds 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 268 helices and 30 sheets defined 50.5% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.919A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.598A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.088A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU E 189 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 194 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.370A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 removed outlier: 4.430A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.934A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.902A pdb=" N ALA E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.546A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.551A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.462A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.784A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.652A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 4.323A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.132A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 437 Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 35 through 40 removed outlier: 3.562A pdb=" N SER N 40 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 58 through 60 No H-bonds generated for 'chain 'N' and resid 58 through 60' Processing helix chain 'N' and resid 68 through 85 Processing helix chain 'N' and resid 93 through 97 Processing helix chain 'N' and resid 101 through 118 Processing helix chain 'N' and resid 126 through 130 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 removed outlier: 3.919A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.599A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.088A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU J 189 " --> pdb=" O ASN J 186 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU J 196 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.370A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 removed outlier: 4.427A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 283 removed outlier: 4.935A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.902A pdb=" N ALA J 400 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 removed outlier: 3.545A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.551A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.461A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.785A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.652A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 280 through 283 Processing helix chain 'G' and resid 288 through 295 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.130A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 437 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.920A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.634A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.599A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.089A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.556A pdb=" N LEU C 189 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU C 196 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.370A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 4.429A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.935A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.903A pdb=" N ALA C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 removed outlier: 3.546A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.552A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.461A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.785A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.651A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 4.325A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 4.133A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 437 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 removed outlier: 3.918A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.598A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.088A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.554A pdb=" N LEU L 189 " --> pdb=" O ASN L 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR L 194 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU L 196 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.371A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 removed outlier: 4.428A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 removed outlier: 4.935A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.901A pdb=" N ALA L 400 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 removed outlier: 3.546A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.553A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 73 through 80 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.461A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.785A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 3.651A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 280 through 283 Processing helix chain 'I' and resid 288 through 295 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 4.131A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 437 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.919A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.634A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.598A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.089A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.556A pdb=" N LEU A 189 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.370A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.431A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.935A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.901A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.546A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.551A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.462A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.785A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.652A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.325A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.133A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 Processing helix chain 'M' and resid 17 through 28 Processing helix chain 'M' and resid 35 through 40 removed outlier: 3.561A pdb=" N SER M 40 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 51 Processing helix chain 'M' and resid 58 through 60 No H-bonds generated for 'chain 'M' and resid 58 through 60' Processing helix chain 'M' and resid 68 through 85 Processing helix chain 'M' and resid 93 through 97 Processing helix chain 'M' and resid 101 through 118 Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.919A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.598A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.089A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.554A pdb=" N LEU K 189 " --> pdb=" O ASN K 186 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 194 " --> pdb=" O THR K 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU K 196 " --> pdb=" O THR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.371A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 removed outlier: 4.430A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.936A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.902A pdb=" N ALA K 400 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 removed outlier: 3.546A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.550A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 73 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.461A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.784A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.652A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 280 through 283 Processing helix chain 'H' and resid 288 through 295 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 removed outlier: 4.131A pdb=" N GLU H 411 " --> pdb=" O TRP H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 437 Processing sheet with id= A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.591A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.015A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.590A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP G 205 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N PHE G 272 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.591A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.591A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP I 205 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N PHE I 272 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.591A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.893A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.591A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.894A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP H 205 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N PHE H 272 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.940A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 1898 hydrogen bonds defined for protein. 4908 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: 17.06 Time building geometry restraints manager: 18.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 14136 1.35 - 1.50: 12108 1.50 - 1.65: 17348 1.65 - 1.81: 417 1.81 - 1.96: 43 Bond restraints: 44052 Sorted by residual: bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.959 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.958 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.957 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" PG GSP F 501 " pdb=" S1G GSP F 501 " ideal model delta sigma weight residual 1.700 1.941 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.940 -0.240 2.00e-02 2.50e+03 1.44e+02 ... (remaining 44047 not shown) Histogram of bond angle deviations from ideal: 98.93 - 106.53: 1645 106.53 - 114.13: 23693 114.13 - 121.73: 22317 121.73 - 129.33: 11863 129.33 - 136.93: 312 Bond angle restraints: 59830 Sorted by residual: angle pdb=" C LYS A 338 " pdb=" N ARG A 339 " pdb=" CA ARG A 339 " ideal model delta sigma weight residual 120.38 128.13 -7.75 1.37e+00 5.33e-01 3.20e+01 angle pdb=" C LYS E 338 " pdb=" N ARG E 339 " pdb=" CA ARG E 339 " ideal model delta sigma weight residual 120.38 128.09 -7.71 1.37e+00 5.33e-01 3.17e+01 angle pdb=" C LYS C 338 " pdb=" N ARG C 339 " pdb=" CA ARG C 339 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.37e+00 5.33e-01 3.14e+01 angle pdb=" C LYS L 338 " pdb=" N ARG L 339 " pdb=" CA ARG L 339 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.37e+00 5.33e-01 3.14e+01 angle pdb=" C LYS J 338 " pdb=" N ARG J 339 " pdb=" CA ARG J 339 " ideal model delta sigma weight residual 120.38 128.02 -7.64 1.37e+00 5.33e-01 3.11e+01 ... (remaining 59825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 25433 33.95 - 67.91: 699 67.91 - 101.86: 42 101.86 - 135.82: 0 135.82 - 169.77: 18 Dihedral angle restraints: 26192 sinusoidal: 10488 harmonic: 15704 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -120.96 -169.77 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.20 -169.53 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.74 -168.99 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 26189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4170 0.065 - 0.131: 1675 0.131 - 0.196: 436 0.196 - 0.262: 208 0.262 - 0.327: 39 Chirality restraints: 6528 Sorted by residual: chirality pdb=" CA ASN F 167 " pdb=" N ASN F 167 " pdb=" C ASN F 167 " pdb=" CB ASN F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASN H 167 " pdb=" N ASN H 167 " pdb=" C ASN H 167 " pdb=" CB ASN H 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ASN B 167 " pdb=" N ASN B 167 " pdb=" C ASN B 167 " pdb=" CB ASN B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 6525 not shown) Planarity restraints: 7782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 117 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C ALA N 117 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA N 117 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN N 118 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 117 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ALA M 117 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA M 117 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN M 118 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " -0.024 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" C2 GTP C 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " -0.004 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " -0.003 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " -0.007 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " -0.004 2.00e-02 2.50e+03 ... (remaining 7779 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 94 2.59 - 3.17: 35478 3.17 - 3.74: 69175 3.74 - 4.32: 96323 4.32 - 4.90: 162869 Nonbonded interactions: 363939 Sorted by model distance: nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 2.010 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.052 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.054 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.056 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.067 2.170 ... (remaining 363934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 6.980 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: 0.030 Extract box with map and model: 28.850 Check model and map are aligned: 0.720 Set scattering table: 0.410 Process input model: 112.300 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.350 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.009 0.259 44052 Z= 0.600 Angle : 1.398 12.615 59830 Z= 0.973 Chirality : 0.082 0.327 6528 Planarity : 0.006 0.043 7782 Dihedral : 15.616 169.773 16112 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.19 % Favored : 97.70 % Rotamer: Outliers : 1.12 % Allowed : 4.71 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.11), residues: 5388 helix: 0.93 (0.09), residues: 2494 sheet: 0.28 (0.18), residues: 816 loop : -0.70 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 21 HIS 0.010 0.002 HIS L 8 PHE 0.020 0.002 PHE H 92 TYR 0.019 0.002 TYR E 224 ARG 0.025 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 992 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 VAL cc_start: 0.8618 (m) cc_final: 0.8271 (t) REVERT: E 357 TYR cc_start: 0.7379 (m-80) cc_final: 0.7175 (m-10) REVERT: F 240 THR cc_start: 0.8845 (t) cc_final: 0.8506 (t) REVERT: F 325 MET cc_start: 0.7678 (mmm) cc_final: 0.7077 (mmm) REVERT: N 113 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7580 (mttt) REVERT: J 172 TYR cc_start: 0.8227 (t80) cc_final: 0.7627 (t80) REVERT: J 339 ARG cc_start: 0.7579 (ptm160) cc_final: 0.6298 (mmm160) REVERT: G 332 MET cc_start: 0.8750 (mmp) cc_final: 0.8464 (mmm) REVERT: C 154 MET cc_start: 0.7680 (mmm) cc_final: 0.7428 (mmm) REVERT: C 313 MET cc_start: 0.8108 (mtm) cc_final: 0.7772 (mtm) REVERT: D 378 ILE cc_start: 0.8577 (mm) cc_final: 0.8313 (mm) REVERT: L 339 ARG cc_start: 0.7461 (ptm160) cc_final: 0.6868 (mmm160) REVERT: I 180 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (p) REVERT: I 204 ILE cc_start: 0.9050 (mp) cc_final: 0.8844 (mt) REVERT: I 414 ASP cc_start: 0.6596 (p0) cc_final: 0.6249 (t70) REVERT: B 90 ASP cc_start: 0.7055 (t70) cc_final: 0.6810 (t0) REVERT: B 101 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8180 (t0) REVERT: B 204 ILE cc_start: 0.8803 (mp) cc_final: 0.8526 (mt) REVERT: B 281 GLN cc_start: 0.8065 (pt0) cc_final: 0.7818 (pt0) REVERT: B 325 MET cc_start: 0.7853 (mmm) cc_final: 0.7302 (mmm) REVERT: B 333 LEU cc_start: 0.9033 (tp) cc_final: 0.8814 (tp) REVERT: M 122 LYS cc_start: 0.6445 (mtpt) cc_final: 0.5966 (mmmm) REVERT: K 154 MET cc_start: 0.8410 (mmm) cc_final: 0.7834 (mmp) REVERT: K 176 GLN cc_start: 0.7420 (mt0) cc_final: 0.7091 (mt0) REVERT: K 313 MET cc_start: 0.8113 (mtm) cc_final: 0.7854 (mtp) REVERT: K 339 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7044 (mmm160) REVERT: H 378 ILE cc_start: 0.8742 (mm) cc_final: 0.8498 (mm) outliers start: 52 outliers final: 10 residues processed: 1035 average time/residue: 0.5915 time to fit residues: 967.4852 Evaluate side-chains 580 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 568 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 224 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 0.9980 chunk 406 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 420 optimal weight: 0.4980 chunk 162 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 312 optimal weight: 0.9980 chunk 486 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 88 HIS E 358 GLN F 6 HIS F 15 GLN F 37 HIS F 281 GLN F 309 HIS F 336 GLN F 406 HIS ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN J 88 HIS J 300 ASN J 358 GLN G 6 HIS G 15 GLN G 101 ASN G 309 HIS G 336 GLN G 433 GLN C 15 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 GLN D 15 GLN D 229 HIS D 281 GLN D 309 HIS D 336 GLN D 349 ASN D 406 HIS L 15 GLN L 358 GLN I 14 ASN I 15 GLN I 59 ASN I 101 ASN I 281 GLN I 309 HIS I 336 GLN A 15 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN B 6 HIS B 15 GLN B 281 GLN B 293 GLN B 309 HIS B 336 GLN B 337 ASN B 406 HIS M 74 ASN K 15 GLN K 300 ASN K 358 GLN H 6 HIS H 15 GLN H 281 GLN H 336 GLN H 406 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44052 Z= 0.194 Angle : 0.577 8.990 59830 Z= 0.299 Chirality : 0.042 0.171 6528 Planarity : 0.005 0.036 7782 Dihedral : 11.048 174.671 6072 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.25 % Allowed : 9.76 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.31 (0.12), residues: 5388 helix: 1.94 (0.11), residues: 2472 sheet: 0.46 (0.18), residues: 822 loop : -0.19 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 110 HIS 0.006 0.001 HIS A 309 PHE 0.014 0.001 PHE H 135 TYR 0.019 0.001 TYR E 172 ARG 0.006 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 629 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7595 (m-80) cc_final: 0.7313 (m-10) REVERT: E 392 ASP cc_start: 0.6493 (m-30) cc_final: 0.6249 (m-30) REVERT: F 259 MET cc_start: 0.7018 (mmm) cc_final: 0.6501 (mmm) REVERT: F 322 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7378 (tpt170) REVERT: F 323 MET cc_start: 0.8008 (ptp) cc_final: 0.7761 (ptp) REVERT: N 113 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7542 (mttt) REVERT: J 339 ARG cc_start: 0.7352 (ptm160) cc_final: 0.6167 (mmm-85) REVERT: C 313 MET cc_start: 0.8049 (mtm) cc_final: 0.7617 (mtm) REVERT: C 339 ARG cc_start: 0.7862 (ptt180) cc_final: 0.6678 (tpt170) REVERT: L 210 TYR cc_start: 0.7997 (m-10) cc_final: 0.7460 (m-10) REVERT: L 339 ARG cc_start: 0.7393 (ptm160) cc_final: 0.6849 (mmm160) REVERT: I 114 LEU cc_start: 0.9293 (tp) cc_final: 0.9061 (tp) REVERT: I 435 TYR cc_start: 0.8101 (m-80) cc_final: 0.7684 (m-10) REVERT: A 308 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7885 (mtm110) REVERT: B 90 ASP cc_start: 0.7275 (t70) cc_final: 0.7004 (t0) REVERT: B 333 LEU cc_start: 0.8901 (tp) cc_final: 0.8619 (tp) REVERT: B 422 GLU cc_start: 0.7526 (tp30) cc_final: 0.7315 (tp30) REVERT: M 122 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5910 (mmmm) REVERT: K 176 GLN cc_start: 0.7517 (mt0) cc_final: 0.7191 (mt0) REVERT: K 313 MET cc_start: 0.8156 (mtm) cc_final: 0.7872 (mtp) REVERT: K 339 ARG cc_start: 0.7546 (ptm160) cc_final: 0.7035 (mmm160) REVERT: H 378 ILE cc_start: 0.8808 (mm) cc_final: 0.8575 (mt) REVERT: H 435 TYR cc_start: 0.7990 (m-80) cc_final: 0.7515 (m-10) outliers start: 58 outliers final: 35 residues processed: 670 average time/residue: 0.5435 time to fit residues: 599.6477 Evaluate side-chains 560 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 525 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 405 optimal weight: 0.3980 chunk 331 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 487 optimal weight: 7.9990 chunk 526 optimal weight: 1.9990 chunk 434 optimal weight: 0.7980 chunk 483 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS E 88 HIS E 186 ASN E 283 HIS F 258 ASN F 293 GLN F 349 ASN J 8 HIS J 186 ASN J 283 HIS G 14 ASN G 258 ASN C 8 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 37 HIS D 258 ASN D 349 ASN L 8 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN I 258 ASN I 309 HIS A 8 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 283 HIS B 258 ASN M 74 ASN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 283 HIS H 258 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 44052 Z= 0.304 Angle : 0.559 9.550 59830 Z= 0.289 Chirality : 0.044 0.156 6528 Planarity : 0.005 0.040 7782 Dihedral : 10.522 177.531 6068 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.10 % Allowed : 11.21 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.09 (0.12), residues: 5388 helix: 1.59 (0.11), residues: 2494 sheet: 0.68 (0.17), residues: 834 loop : -0.25 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 346 HIS 0.008 0.001 HIS C 28 PHE 0.016 0.002 PHE M 63 TYR 0.016 0.001 TYR A 172 ARG 0.004 0.000 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 556 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7769 (m-80) cc_final: 0.7453 (m-10) REVERT: E 392 ASP cc_start: 0.6407 (m-30) cc_final: 0.6025 (m-30) REVERT: F 422 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7510 (tp30) REVERT: J 26 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8306 (mm) REVERT: J 308 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7983 (ptp-170) REVERT: J 339 ARG cc_start: 0.7659 (ptm160) cc_final: 0.6505 (mmm160) REVERT: C 339 ARG cc_start: 0.7990 (ptt180) cc_final: 0.6734 (tpt170) REVERT: C 433 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7474 (tm-30) REVERT: L 309 HIS cc_start: 0.7344 (m90) cc_final: 0.7134 (m90) REVERT: L 339 ARG cc_start: 0.7502 (ptm160) cc_final: 0.7019 (mmm160) REVERT: I 414 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7213 (p0) REVERT: I 435 TYR cc_start: 0.8187 (m-80) cc_final: 0.7747 (m-10) REVERT: A 398 MET cc_start: 0.7863 (mtp) cc_final: 0.7320 (mtm) REVERT: B 90 ASP cc_start: 0.7429 (t70) cc_final: 0.7158 (t0) REVERT: M 85 MET cc_start: 0.8060 (mmp) cc_final: 0.7858 (mmp) REVERT: M 122 LYS cc_start: 0.6371 (mtpt) cc_final: 0.6002 (mmmm) REVERT: K 339 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7234 (mmm160) REVERT: H 435 TYR cc_start: 0.7933 (m-80) cc_final: 0.7411 (m-10) outliers start: 97 outliers final: 58 residues processed: 630 average time/residue: 0.5400 time to fit residues: 562.8229 Evaluate side-chains 540 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 480 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 414 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 302 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 232 optimal weight: 0.2980 chunk 327 optimal weight: 3.9990 chunk 489 optimal weight: 0.8980 chunk 518 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 463 optimal weight: 0.0370 chunk 139 optimal weight: 0.0570 overall best weight: 1.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 229 HIS F 293 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44052 Z= 0.174 Angle : 0.507 10.345 59830 Z= 0.257 Chirality : 0.041 0.163 6528 Planarity : 0.004 0.036 7782 Dihedral : 10.166 173.158 6064 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.01 % Allowed : 12.20 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.12), residues: 5388 helix: 1.63 (0.11), residues: 2488 sheet: 0.57 (0.17), residues: 858 loop : -0.07 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 388 HIS 0.006 0.001 HIS F 229 PHE 0.014 0.001 PHE E 169 TYR 0.013 0.001 TYR L 172 ARG 0.013 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 550 time to evaluate : 4.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7726 (m-80) cc_final: 0.7396 (m-10) REVERT: E 392 ASP cc_start: 0.6377 (m-30) cc_final: 0.6090 (m-30) REVERT: F 422 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7470 (tp30) REVERT: J 26 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8207 (mm) REVERT: J 308 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7845 (ptp-170) REVERT: J 339 ARG cc_start: 0.7600 (ptm160) cc_final: 0.6578 (tpt170) REVERT: C 335 ILE cc_start: 0.8844 (mm) cc_final: 0.8488 (mm) REVERT: C 339 ARG cc_start: 0.8000 (ptt180) cc_final: 0.6726 (tpt170) REVERT: C 433 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7376 (tm-30) REVERT: L 339 ARG cc_start: 0.7442 (ptm160) cc_final: 0.7084 (tpt170) REVERT: A 113 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 398 MET cc_start: 0.7906 (mtp) cc_final: 0.7333 (mtm) REVERT: B 90 ASP cc_start: 0.7279 (t70) cc_final: 0.7040 (t0) REVERT: B 435 TYR cc_start: 0.8183 (m-10) cc_final: 0.7973 (m-10) REVERT: M 122 LYS cc_start: 0.6425 (mtpt) cc_final: 0.6020 (mmmm) REVERT: K 339 ARG cc_start: 0.7630 (ptm160) cc_final: 0.7221 (mmm160) REVERT: H 254 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8459 (mtpt) outliers start: 93 outliers final: 52 residues processed: 618 average time/residue: 0.5446 time to fit residues: 559.0224 Evaluate side-chains 551 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 497 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 124 TYR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 124 TYR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 442 optimal weight: 9.9990 chunk 358 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 465 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN F 15 GLN F 293 GLN G 281 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS L 88 HIS L 301 GLN L 309 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44052 Z= 0.263 Angle : 0.523 9.049 59830 Z= 0.266 Chirality : 0.042 0.156 6528 Planarity : 0.004 0.038 7782 Dihedral : 9.935 171.070 6061 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.40 % Allowed : 12.12 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.06 (0.12), residues: 5388 helix: 1.42 (0.11), residues: 2524 sheet: 0.68 (0.17), residues: 834 loop : -0.09 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 388 HIS 0.007 0.001 HIS K 309 PHE 0.027 0.001 PHE D 262 TYR 0.027 0.001 TYR D 435 ARG 0.006 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 532 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7823 (m-80) cc_final: 0.7475 (m-10) REVERT: F 422 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7527 (tp30) REVERT: N 50 MET cc_start: 0.7138 (mtp) cc_final: 0.6912 (ttm) REVERT: J 26 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8143 (mm) REVERT: J 339 ARG cc_start: 0.7745 (ptm160) cc_final: 0.6563 (mmm160) REVERT: C 339 ARG cc_start: 0.8004 (ptt180) cc_final: 0.6718 (tpt170) REVERT: C 433 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7432 (tm-30) REVERT: L 339 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7169 (tpt170) REVERT: A 398 MET cc_start: 0.8055 (mtp) cc_final: 0.7661 (mtm) REVERT: B 90 ASP cc_start: 0.7334 (t70) cc_final: 0.7101 (t0) REVERT: M 50 MET cc_start: 0.7231 (ttm) cc_final: 0.6977 (mtp) REVERT: M 122 LYS cc_start: 0.6385 (mtpt) cc_final: 0.6064 (mmmm) REVERT: K 203 MET cc_start: 0.7932 (mmm) cc_final: 0.7431 (mmm) REVERT: K 339 ARG cc_start: 0.7761 (ptm160) cc_final: 0.7264 (tpt170) REVERT: H 254 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8501 (mtpt) REVERT: H 332 MET cc_start: 0.8515 (mmm) cc_final: 0.8226 (mmm) outliers start: 111 outliers final: 79 residues processed: 609 average time/residue: 0.5564 time to fit residues: 559.4549 Evaluate side-chains 586 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 505 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 9.9990 chunk 466 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 518 optimal weight: 5.9990 chunk 430 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 171 optimal weight: 0.4980 chunk 272 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN F 334 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN A 18 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44052 Z= 0.209 Angle : 0.503 10.195 59830 Z= 0.254 Chirality : 0.041 0.157 6528 Planarity : 0.004 0.038 7782 Dihedral : 9.671 166.659 6060 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.53 % Allowed : 12.61 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.08 (0.12), residues: 5388 helix: 1.41 (0.11), residues: 2524 sheet: 0.72 (0.17), residues: 834 loop : -0.07 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 388 HIS 0.004 0.001 HIS F 229 PHE 0.023 0.001 PHE M 52 TYR 0.021 0.001 TYR B 435 ARG 0.004 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 526 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7841 (m-80) cc_final: 0.7453 (m-10) REVERT: F 422 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7493 (tp30) REVERT: N 50 MET cc_start: 0.7047 (mtp) cc_final: 0.6718 (mtp) REVERT: J 26 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8178 (mm) REVERT: J 339 ARG cc_start: 0.7731 (ptm160) cc_final: 0.6570 (mmm160) REVERT: C 339 ARG cc_start: 0.8007 (ptt180) cc_final: 0.6701 (tpt170) REVERT: C 433 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7412 (tm-30) REVERT: L 339 ARG cc_start: 0.7657 (ptm160) cc_final: 0.7167 (tpt170) REVERT: A 398 MET cc_start: 0.8052 (mtp) cc_final: 0.7654 (mtm) REVERT: M 122 LYS cc_start: 0.6453 (mtpt) cc_final: 0.6159 (mmmm) REVERT: K 203 MET cc_start: 0.8039 (mmm) cc_final: 0.7493 (mmm) REVERT: K 339 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7268 (tpt170) REVERT: H 254 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: H 413 MET cc_start: 0.8535 (ttm) cc_final: 0.8185 (ttm) outliers start: 117 outliers final: 86 residues processed: 598 average time/residue: 0.5329 time to fit residues: 527.5797 Evaluate side-chains 583 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 495 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 299 LYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 436 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 516 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 314 optimal weight: 0.0010 chunk 238 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 44052 Z= 0.241 Angle : 0.512 9.346 59830 Z= 0.259 Chirality : 0.042 0.154 6528 Planarity : 0.004 0.039 7782 Dihedral : 9.471 162.838 6060 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.51 % Allowed : 12.98 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.01 (0.12), residues: 5388 helix: 1.33 (0.11), residues: 2530 sheet: 0.76 (0.18), residues: 804 loop : -0.08 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 388 HIS 0.004 0.001 HIS L 309 PHE 0.023 0.001 PHE M 52 TYR 0.027 0.001 TYR N 124 ARG 0.008 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 517 time to evaluate : 5.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7874 (m-80) cc_final: 0.7468 (m-10) REVERT: F 422 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7484 (tp30) REVERT: N 50 MET cc_start: 0.6867 (mtp) cc_final: 0.6502 (mmm) REVERT: N 122 LYS cc_start: 0.5945 (mtpt) cc_final: 0.5341 (mmmt) REVERT: J 26 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8167 (mm) REVERT: J 339 ARG cc_start: 0.7807 (ptm160) cc_final: 0.6642 (mmm160) REVERT: C 339 ARG cc_start: 0.8038 (ptt180) cc_final: 0.6750 (tpt170) REVERT: C 433 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7416 (tm-30) REVERT: L 339 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7212 (tpt170) REVERT: A 398 MET cc_start: 0.8020 (mtp) cc_final: 0.7600 (mtm) REVERT: M 122 LYS cc_start: 0.6549 (mtpt) cc_final: 0.6060 (mmmm) REVERT: K 203 MET cc_start: 0.8067 (mmm) cc_final: 0.7509 (mmm) REVERT: K 339 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7301 (tpt170) REVERT: H 254 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8545 (mtpt) REVERT: H 413 MET cc_start: 0.8592 (ttm) cc_final: 0.8277 (ttm) outliers start: 116 outliers final: 95 residues processed: 589 average time/residue: 0.5463 time to fit residues: 532.1797 Evaluate side-chains 589 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 492 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 0.8980 chunk 206 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 328 optimal weight: 40.0000 chunk 351 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN I 229 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 44052 Z= 0.221 Angle : 0.505 10.211 59830 Z= 0.255 Chirality : 0.041 0.147 6528 Planarity : 0.004 0.040 7782 Dihedral : 9.213 157.586 6060 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.46 % Allowed : 13.33 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.00 (0.12), residues: 5388 helix: 1.32 (0.11), residues: 2530 sheet: 0.75 (0.18), residues: 804 loop : -0.10 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 388 HIS 0.004 0.001 HIS F 229 PHE 0.023 0.001 PHE M 52 TYR 0.020 0.001 TYR D 435 ARG 0.007 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 524 time to evaluate : 5.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7861 (m-80) cc_final: 0.7474 (m-10) REVERT: N 122 LYS cc_start: 0.6111 (mtpt) cc_final: 0.5455 (mmmt) REVERT: J 26 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8163 (mm) REVERT: J 339 ARG cc_start: 0.7878 (ptm160) cc_final: 0.6709 (mmm160) REVERT: G 323 MET cc_start: 0.7997 (ptp) cc_final: 0.7692 (ptp) REVERT: C 339 ARG cc_start: 0.7956 (ptt180) cc_final: 0.6663 (tpt170) REVERT: C 433 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 26 ASP cc_start: 0.7466 (t0) cc_final: 0.7258 (t0) REVERT: L 339 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7198 (tpt170) REVERT: A 24 TYR cc_start: 0.8704 (m-10) cc_final: 0.8327 (m-10) REVERT: A 398 MET cc_start: 0.8004 (mtp) cc_final: 0.7581 (mtm) REVERT: M 122 LYS cc_start: 0.6599 (mtpt) cc_final: 0.6170 (mmmm) REVERT: K 339 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7323 (tpt170) REVERT: K 388 TRP cc_start: 0.8726 (m100) cc_final: 0.8393 (m100) REVERT: H 75 MET cc_start: 0.7943 (mmm) cc_final: 0.7631 (mmm) REVERT: H 413 MET cc_start: 0.8609 (ttm) cc_final: 0.8268 (ttm) outliers start: 114 outliers final: 100 residues processed: 600 average time/residue: 0.5372 time to fit residues: 533.4077 Evaluate side-chains 604 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 503 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 5.9990 chunk 494 optimal weight: 7.9990 chunk 451 optimal weight: 10.0000 chunk 481 optimal weight: 7.9990 chunk 289 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 378 optimal weight: 0.0570 chunk 147 optimal weight: 0.8980 chunk 435 optimal weight: 0.8980 chunk 455 optimal weight: 3.9990 chunk 479 optimal weight: 7.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 HIS F 293 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 37 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 44052 Z= 0.157 Angle : 0.489 11.065 59830 Z= 0.246 Chirality : 0.041 0.146 6528 Planarity : 0.004 0.039 7782 Dihedral : 8.900 150.916 6060 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 13.91 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.14 (0.12), residues: 5388 helix: 1.44 (0.11), residues: 2506 sheet: 0.90 (0.18), residues: 786 loop : -0.04 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.007 0.001 HIS F 229 PHE 0.022 0.001 PHE M 52 TYR 0.013 0.001 TYR M 32 ARG 0.007 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 547 time to evaluate : 5.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7852 (m-80) cc_final: 0.7461 (m-10) REVERT: N 83 LYS cc_start: 0.8290 (tttt) cc_final: 0.7934 (tptp) REVERT: J 26 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8241 (mm) REVERT: J 339 ARG cc_start: 0.7794 (ptm160) cc_final: 0.6796 (tpt170) REVERT: G 323 MET cc_start: 0.7895 (ptp) cc_final: 0.7651 (ptp) REVERT: C 339 ARG cc_start: 0.8007 (ptt180) cc_final: 0.6669 (tpt170) REVERT: C 433 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 26 ASP cc_start: 0.7406 (t0) cc_final: 0.7196 (t0) REVERT: L 339 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7168 (tpt170) REVERT: A 24 TYR cc_start: 0.8617 (m-10) cc_final: 0.8243 (m-10) REVERT: A 398 MET cc_start: 0.7970 (mtp) cc_final: 0.7564 (mtm) REVERT: B 3 GLU cc_start: 0.7351 (mp0) cc_final: 0.7133 (mt-10) REVERT: B 411 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7017 (mm-30) REVERT: M 122 LYS cc_start: 0.6474 (mtpt) cc_final: 0.6076 (mmmm) REVERT: K 339 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7292 (tpt170) REVERT: K 388 TRP cc_start: 0.8704 (m100) cc_final: 0.8458 (m100) REVERT: H 75 MET cc_start: 0.7920 (mmm) cc_final: 0.7610 (mmm) REVERT: H 413 MET cc_start: 0.8570 (ttm) cc_final: 0.8228 (ttm) outliers start: 92 outliers final: 76 residues processed: 603 average time/residue: 0.5405 time to fit residues: 539.3874 Evaluate side-chains 591 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 514 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 1.9990 chunk 509 optimal weight: 0.9980 chunk 310 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 533 optimal weight: 0.9980 chunk 491 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 328 optimal weight: 40.0000 chunk 260 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44052 Z= 0.203 Angle : 0.504 11.374 59830 Z= 0.253 Chirality : 0.041 0.145 6528 Planarity : 0.004 0.040 7782 Dihedral : 8.801 147.923 6060 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.92 % Allowed : 14.36 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.10 (0.12), residues: 5388 helix: 1.44 (0.11), residues: 2500 sheet: 0.84 (0.18), residues: 804 loop : -0.09 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 388 HIS 0.003 0.001 HIS L 309 PHE 0.021 0.001 PHE M 52 TYR 0.013 0.001 TYR D 435 ARG 0.008 0.000 ARG C 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 518 time to evaluate : 4.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 357 TYR cc_start: 0.7880 (m-80) cc_final: 0.7485 (m-10) REVERT: N 83 LYS cc_start: 0.8323 (tttt) cc_final: 0.7940 (tptp) REVERT: J 26 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8270 (mm) REVERT: J 339 ARG cc_start: 0.7820 (ptm160) cc_final: 0.6770 (mmm160) REVERT: G 323 MET cc_start: 0.7938 (ptp) cc_final: 0.7658 (ptp) REVERT: C 339 ARG cc_start: 0.8036 (ptt180) cc_final: 0.6681 (tpt170) REVERT: C 433 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 26 ASP cc_start: 0.7420 (t0) cc_final: 0.7199 (t0) REVERT: L 339 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7196 (tpt170) REVERT: A 24 TYR cc_start: 0.8688 (m-10) cc_final: 0.8312 (m-10) REVERT: A 398 MET cc_start: 0.7991 (mtp) cc_final: 0.7590 (mtm) REVERT: B 3 GLU cc_start: 0.7471 (mp0) cc_final: 0.7237 (mt-10) REVERT: B 411 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7059 (mm-30) REVERT: M 122 LYS cc_start: 0.6477 (mtpt) cc_final: 0.5976 (mmmt) REVERT: K 2 ARG cc_start: 0.3821 (mtt90) cc_final: 0.3429 (mpt90) REVERT: K 339 ARG cc_start: 0.7833 (ptm160) cc_final: 0.7336 (tpt170) REVERT: K 388 TRP cc_start: 0.8682 (m100) cc_final: 0.8298 (m100) REVERT: H 413 MET cc_start: 0.8587 (ttm) cc_final: 0.8241 (ttm) outliers start: 89 outliers final: 84 residues processed: 576 average time/residue: 0.5416 time to fit residues: 515.1190 Evaluate side-chains 598 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 513 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 302 MET Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 SER Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 1.9990 chunk 452 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 437 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS A 88 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087393 restraints weight = 69603.280| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.15 r_work: 0.3179 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 44052 Z= 0.186 Angle : 0.497 11.302 59830 Z= 0.249 Chirality : 0.041 0.146 6528 Planarity : 0.004 0.040 7782 Dihedral : 8.647 143.175 6060 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.86 % Allowed : 14.54 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.11 (0.12), residues: 5388 helix: 1.44 (0.11), residues: 2500 sheet: 0.84 (0.18), residues: 804 loop : -0.08 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 388 HIS 0.003 0.001 HIS L 309 PHE 0.022 0.001 PHE M 52 TYR 0.013 0.001 TYR D 435 ARG 0.009 0.000 ARG C 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10507.53 seconds wall clock time: 190 minutes 13.75 seconds (11413.75 seconds total)