Starting phenix.real_space_refine on Mon Mar 18 23:01:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bq2_16170/03_2024/8bq2_16170_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 Ca 18 9.91 5 P 57 5.49 5 S 117 5.16 5 C 13791 2.51 5 N 3975 2.21 5 O 4373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22331 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "E" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "G" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "H" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "W" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 650 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.37, per 1000 atoms: 0.51 Number of scatterers: 22331 At special positions: 0 Unit cell: (114.4, 117.26, 217.36, 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) Ca 18 19.99 S 117 16.00 P 57 15.00 O 4373 8.00 N 3975 7.00 C 13791 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: 8.24 Conformation dependent library (CDL) restraints added in 4.0 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 18 sheets defined 45.5% alpha, 16.1% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 8.86 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.175A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 No H-bonds generated for 'chain 'A' and resid 182 through 185' Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 242 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET A 243 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.677A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.175A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER B 239 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 242 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET B 243 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 4.175A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 185 No H-bonds generated for 'chain 'C' and resid 182 through 185' Processing helix chain 'C' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER C 239 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN C 242 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET C 243 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 133 through 145 removed outlier: 4.174A pdb=" N CYS D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 185 No H-bonds generated for 'chain 'D' and resid 182 through 185' Processing helix chain 'D' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 235 through 259 removed outlier: 4.469A pdb=" N SER D 239 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET D 243 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 259 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 31 Processing helix chain 'E' and resid 35 through 43 removed outlier: 3.636A pdb=" N LYS E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 133 through 145 removed outlier: 4.174A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 185 No H-bonds generated for 'chain 'E' and resid 182 through 185' Processing helix chain 'E' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 235 through 259 removed outlier: 4.469A pdb=" N SER E 239 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 243 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE E 259 " --> pdb=" O ALA E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.677A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.730A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 133 through 145 removed outlier: 4.174A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 185 No H-bonds generated for 'chain 'F' and resid 182 through 185' Processing helix chain 'F' and resid 197 through 213 removed outlier: 4.009A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 No H-bonds generated for 'chain 'F' and resid 228 through 231' Processing helix chain 'F' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER F 239 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN F 242 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET F 243 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE F 259 " --> pdb=" O ALA F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 133 through 145 removed outlier: 4.174A pdb=" N CYS G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.510A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 185 No H-bonds generated for 'chain 'G' and resid 182 through 185' Processing helix chain 'G' and resid 197 through 213 removed outlier: 4.009A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 235 through 259 removed outlier: 4.469A pdb=" N SER G 239 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET G 243 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE G 259 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 31 Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.637A pdb=" N LYS H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 removed outlier: 4.044A pdb=" N GLU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 133 through 145 removed outlier: 4.175A pdb=" N CYS H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 150 No H-bonds generated for 'chain 'H' and resid 148 through 150' Processing helix chain 'H' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 185 No H-bonds generated for 'chain 'H' and resid 182 through 185' Processing helix chain 'H' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 231 No H-bonds generated for 'chain 'H' and resid 228 through 231' Processing helix chain 'H' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER H 239 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN H 242 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET H 243 " --> pdb=" O ALA H 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE H 259 " --> pdb=" O ALA H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA H 293 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 35 through 43 removed outlier: 3.636A pdb=" N LYS I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.731A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 4.043A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 133 through 145 removed outlier: 4.175A pdb=" N CYS I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 168 through 178 removed outlier: 3.511A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 185 No H-bonds generated for 'chain 'I' and resid 182 through 185' Processing helix chain 'I' and resid 197 through 213 removed outlier: 4.008A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 231 No H-bonds generated for 'chain 'I' and resid 228 through 231' Processing helix chain 'I' and resid 235 through 259 removed outlier: 4.468A pdb=" N SER I 239 " --> pdb=" O GLY I 236 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN I 242 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET I 243 " --> pdb=" O ALA I 240 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE I 259 " --> pdb=" O ALA I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.678A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 298 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY A 127 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN A 267 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= C, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 298 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLY B 127 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN B 267 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 262 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= E, first strand: chain 'C' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 298 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLY C 127 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN C 267 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 262 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 269 through 271 Processing sheet with id= G, first strand: chain 'D' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 298 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 263 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N MET D 125 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 265 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY D 127 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN D 267 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 262 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS D 156 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU D 219 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET D 158 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL D 221 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 160 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 269 through 271 Processing sheet with id= I, first strand: chain 'E' and resid 333 through 335 removed outlier: 6.453A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 298 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL E 263 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET E 125 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE E 265 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLY E 127 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN E 267 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 262 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL E 221 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 160 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 269 through 271 Processing sheet with id= K, first strand: chain 'F' and resid 333 through 335 removed outlier: 6.453A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 298 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL F 263 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET F 125 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 265 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY F 127 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN F 267 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 262 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS F 156 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU F 219 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET F 158 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL F 221 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 160 " --> pdb=" O VAL F 221 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 269 through 271 Processing sheet with id= M, first strand: chain 'G' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR G 298 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL G 263 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET G 125 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE G 265 " --> pdb=" O MET G 125 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY G 127 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN G 267 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS G 156 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 219 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET G 158 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL G 221 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE G 160 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 269 through 271 Processing sheet with id= O, first strand: chain 'H' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 298 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL H 263 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET H 125 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE H 265 " --> pdb=" O MET H 125 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLY H 127 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN H 267 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 262 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS H 156 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 219 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 158 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL H 221 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 160 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 269 through 271 Processing sheet with id= Q, first strand: chain 'I' and resid 333 through 335 removed outlier: 6.452A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR I 298 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL I 263 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N MET I 125 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE I 265 " --> pdb=" O MET I 125 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLY I 127 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN I 267 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 262 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS I 156 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU I 219 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET I 158 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL I 221 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE I 160 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 269 through 271 828 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 8.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7448 1.34 - 1.46: 4142 1.46 - 1.57: 10843 1.57 - 1.69: 104 1.69 - 1.81: 189 Bond restraints: 22726 Sorted by residual: bond pdb=" O4' DG W 14 " pdb=" C1' DG W 14 " ideal model delta sigma weight residual 1.414 1.449 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" O5' DG W 29 " pdb=" C5' DG W 29 " ideal model delta sigma weight residual 1.423 1.473 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" C5' DG W 29 " pdb=" C4' DG W 29 " ideal model delta sigma weight residual 1.518 1.551 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CB ARG G 235 " pdb=" CG ARG G 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB ARG B 235 " pdb=" CG ARG B 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 22721 not shown) Histogram of bond angle deviations from ideal: 99.71 - 107.75: 997 107.75 - 115.78: 14112 115.78 - 123.82: 15121 123.82 - 131.85: 588 131.85 - 139.89: 37 Bond angle restraints: 30855 Sorted by residual: angle pdb=" O4' DG W 20 " pdb=" C1' DG W 20 " pdb=" N9 DG W 20 " ideal model delta sigma weight residual 108.40 99.97 8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" O3' DG W 29 " pdb=" C3' DG W 29 " pdb=" C2' DG W 29 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA ARG G 27 " pdb=" CB ARG G 27 " pdb=" CG ARG G 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA ARG B 27 " pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA ARG H 27 " pdb=" CB ARG H 27 " pdb=" CG ARG H 27 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 ... (remaining 30850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 12434 16.69 - 33.37: 977 33.37 - 50.06: 283 50.06 - 66.74: 136 66.74 - 83.43: 52 Dihedral angle restraints: 13882 sinusoidal: 5926 harmonic: 7956 Sorted by residual: dihedral pdb=" CA ARG G 95 " pdb=" CB ARG G 95 " pdb=" CG ARG G 95 " pdb=" CD ARG G 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.32 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " pdb=" CG ARG B 95 " pdb=" CD ARG B 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.31 59.31 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG E 95 " pdb=" CB ARG E 95 " pdb=" CG ARG E 95 " pdb=" CD ARG E 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.30 59.30 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2950 0.053 - 0.106: 474 0.106 - 0.158: 79 0.158 - 0.211: 0 0.211 - 0.264: 1 Chirality restraints: 3504 Sorted by residual: chirality pdb=" P DA W 6 " pdb=" OP1 DA W 6 " pdb=" OP2 DA W 6 " pdb=" O5' DA W 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.08 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1' DG W 20 " pdb=" O4' DG W 20 " pdb=" C2' DG W 20 " pdb=" N9 DG W 20 " both_signs ideal model delta sigma weight residual False 2.42 2.56 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE G 160 " pdb=" N ILE G 160 " pdb=" C ILE G 160 " pdb=" CB ILE G 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 3501 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG W 20 " -0.046 2.00e-02 2.50e+03 4.33e-02 5.63e+01 pdb=" N9 DG W 20 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG W 20 " -0.062 2.00e-02 2.50e+03 pdb=" N7 DG W 20 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG W 20 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DG W 20 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG W 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG W 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG W 20 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG W 20 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DG W 20 " 0.058 2.00e-02 2.50e+03 pdb=" C4 DG W 20 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 17 " -0.042 2.00e-02 2.50e+03 4.30e-02 5.54e+01 pdb=" N9 DG W 17 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG W 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG W 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG W 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG W 17 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG W 17 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG W 17 " -0.045 2.00e-02 2.50e+03 pdb=" N3 DG W 17 " 0.131 2.00e-02 2.50e+03 pdb=" C4 DG W 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 4 " 0.020 2.00e-02 2.50e+03 4.02e-02 4.85e+01 pdb=" N9 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DG W 4 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG W 4 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG W 4 " -0.045 2.00e-02 2.50e+03 pdb=" C6 DG W 4 " 0.064 2.00e-02 2.50e+03 pdb=" O6 DG W 4 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG W 4 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG W 4 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DG W 4 " 0.075 2.00e-02 2.50e+03 pdb=" C4 DG W 4 " -0.079 2.00e-02 2.50e+03 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3152 2.76 - 3.29: 20723 3.29 - 3.83: 35203 3.83 - 4.36: 42883 4.36 - 4.90: 73879 Nonbonded interactions: 175840 Sorted by model distance: nonbonded pdb=" OG1 THR B 103 " pdb=" OD2 ASP B 110 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR D 103 " pdb=" OD2 ASP D 110 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR E 103 " pdb=" OD2 ASP E 110 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR A 103 " pdb=" OD2 ASP A 110 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR C 103 " pdb=" OD2 ASP C 110 " model vdw 2.220 2.440 ... (remaining 175835 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' and (resid 21 through 339 or resid 401 through 402)) selection = (chain 'B' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'C' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'D' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'E' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'F' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'G' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'H' and (resid 21 through 339 or resid 400 through 401)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.980 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 62.030 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.003 0.050 22726 Z= 0.163 Angle : 0.543 8.428 30855 Z= 0.315 Chirality : 0.039 0.264 3504 Planarity : 0.006 0.061 3846 Dihedral : 15.173 83.429 8788 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.37 (0.15), residues: 2754 helix: -0.20 (0.14), residues: 1260 sheet: 2.47 (0.24), residues: 468 loop : -1.59 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.003 HIS F 47 PHE 0.015 0.002 PHE F 195 TYR 0.018 0.002 TYR F 228 ARG 0.023 0.002 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8045 (mmm) cc_final: 0.7698 (mtt) REVERT: A 253 LEU cc_start: 0.9290 (tp) cc_final: 0.8935 (tt) REVERT: B 36 ASN cc_start: 0.7169 (t0) cc_final: 0.6961 (t0) REVERT: B 158 MET cc_start: 0.8276 (ttm) cc_final: 0.8064 (ttm) REVERT: C 36 ASN cc_start: 0.8119 (t0) cc_final: 0.7892 (t0) REVERT: C 251 MET cc_start: 0.8038 (tpp) cc_final: 0.7747 (tpt) REVERT: E 36 ASN cc_start: 0.7981 (t0) cc_final: 0.7720 (t0) REVERT: E 222 ASP cc_start: 0.8265 (t0) cc_final: 0.7925 (t70) REVERT: E 326 MET cc_start: 0.8111 (ttm) cc_final: 0.7894 (ttt) REVERT: I 34 ASN cc_start: 0.8241 (p0) cc_final: 0.7990 (p0) REVERT: I 62 ASN cc_start: 0.8303 (m-40) cc_final: 0.7780 (m110) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3908 time to fit residues: 114.3142 Evaluate side-chains 113 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22726 Z= 0.236 Angle : 0.505 5.727 30855 Z= 0.272 Chirality : 0.040 0.131 3504 Planarity : 0.004 0.036 3846 Dihedral : 13.242 80.500 3694 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 7.89 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.44 (0.15), residues: 2754 helix: -0.34 (0.14), residues: 1278 sheet: 2.89 (0.24), residues: 441 loop : -1.65 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 199 PHE 0.019 0.001 PHE C 259 TYR 0.016 0.001 TYR C 315 ARG 0.005 0.000 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8513 (mmm) cc_final: 0.8169 (mtt) REVERT: B 84 MET cc_start: 0.8319 (mmm) cc_final: 0.7999 (mtt) REVERT: D 27 ARG cc_start: 0.7116 (tpp-160) cc_final: 0.6797 (tpm170) REVERT: E 36 ASN cc_start: 0.8236 (t0) cc_final: 0.7770 (t0) REVERT: E 243 MET cc_start: 0.7884 (tpp) cc_final: 0.7524 (tpp) REVERT: E 326 MET cc_start: 0.8146 (ttm) cc_final: 0.7933 (ttt) REVERT: F 72 ASP cc_start: 0.7545 (m-30) cc_final: 0.7275 (m-30) REVERT: I 62 ASN cc_start: 0.8390 (m-40) cc_final: 0.7833 (m-40) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.3322 time to fit residues: 72.8622 Evaluate side-chains 123 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22726 Z= 0.241 Angle : 0.480 6.522 30855 Z= 0.256 Chirality : 0.040 0.130 3504 Planarity : 0.004 0.031 3846 Dihedral : 13.050 88.007 3694 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.21 % Allowed : 9.01 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2754 helix: -0.29 (0.14), residues: 1278 sheet: 2.61 (0.26), residues: 423 loop : -1.54 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 244 PHE 0.014 0.001 PHE A 327 TYR 0.019 0.001 TYR C 315 ARG 0.008 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8476 (mmm) cc_final: 0.8144 (mtt) REVERT: D 27 ARG cc_start: 0.7221 (tpp-160) cc_final: 0.6721 (tpm170) REVERT: E 36 ASN cc_start: 0.8132 (t0) cc_final: 0.7808 (t0) REVERT: F 72 ASP cc_start: 0.7624 (m-30) cc_final: 0.7365 (m-30) REVERT: F 222 ASP cc_start: 0.8243 (t0) cc_final: 0.7923 (t70) REVERT: I 62 ASN cc_start: 0.8283 (m-40) cc_final: 0.7621 (m-40) outliers start: 27 outliers final: 13 residues processed: 142 average time/residue: 0.3580 time to fit residues: 79.4351 Evaluate side-chains 122 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22726 Z= 0.293 Angle : 0.502 7.775 30855 Z= 0.266 Chirality : 0.040 0.127 3504 Planarity : 0.004 0.041 3846 Dihedral : 13.141 80.776 3694 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.30 % Allowed : 9.68 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.56 (0.16), residues: 2754 helix: -0.31 (0.14), residues: 1296 sheet: 2.37 (0.26), residues: 423 loop : -1.59 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 244 PHE 0.023 0.002 PHE I 259 TYR 0.019 0.001 TYR D 315 ARG 0.007 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8611 (mmm) cc_final: 0.8256 (mtt) REVERT: E 36 ASN cc_start: 0.8104 (t0) cc_final: 0.7847 (t0) REVERT: E 326 MET cc_start: 0.7969 (ttt) cc_final: 0.7743 (mtp) REVERT: F 222 ASP cc_start: 0.8318 (t0) cc_final: 0.7998 (t70) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.3574 time to fit residues: 75.6573 Evaluate side-chains 131 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22726 Z= 0.420 Angle : 0.584 9.090 30855 Z= 0.304 Chirality : 0.042 0.142 3504 Planarity : 0.004 0.055 3846 Dihedral : 13.402 83.323 3694 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.48 % Allowed : 9.63 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.71 (0.16), residues: 2754 helix: -0.35 (0.14), residues: 1278 sheet: 2.07 (0.26), residues: 423 loop : -1.65 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 244 PHE 0.020 0.002 PHE G 248 TYR 0.024 0.002 TYR F 315 ARG 0.009 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8651 (mmm) cc_final: 0.8284 (mtt) REVERT: D 27 ARG cc_start: 0.7262 (tpp-160) cc_final: 0.6938 (tpm170) REVERT: E 28 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8493 (mt) REVERT: E 36 ASN cc_start: 0.8542 (t0) cc_final: 0.7826 (t0) REVERT: F 222 ASP cc_start: 0.8270 (t0) cc_final: 0.8054 (t70) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.3379 time to fit residues: 73.4886 Evaluate side-chains 130 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22726 Z= 0.169 Angle : 0.436 9.343 30855 Z= 0.234 Chirality : 0.039 0.139 3504 Planarity : 0.003 0.029 3846 Dihedral : 12.766 87.631 3694 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.12 % Allowed : 10.44 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.60 (0.16), residues: 2754 helix: -0.20 (0.14), residues: 1287 sheet: 2.12 (0.26), residues: 423 loop : -1.68 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 244 PHE 0.010 0.001 PHE A 327 TYR 0.010 0.001 TYR C 315 ARG 0.006 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8525 (mmm) cc_final: 0.8223 (mtt) REVERT: E 36 ASN cc_start: 0.8557 (t0) cc_final: 0.7950 (t0) REVERT: F 72 ASP cc_start: 0.7813 (m-30) cc_final: 0.7578 (m-30) outliers start: 25 outliers final: 18 residues processed: 130 average time/residue: 0.3536 time to fit residues: 72.7533 Evaluate side-chains 127 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22726 Z= 0.338 Angle : 0.523 9.569 30855 Z= 0.275 Chirality : 0.041 0.132 3504 Planarity : 0.004 0.059 3846 Dihedral : 13.020 87.676 3694 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.39 % Allowed : 10.53 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.68 (0.16), residues: 2754 helix: -0.26 (0.14), residues: 1296 sheet: 1.99 (0.26), residues: 423 loop : -1.71 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 244 PHE 0.015 0.002 PHE A 248 TYR 0.018 0.001 TYR D 315 ARG 0.010 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8442 (t0) cc_final: 0.8226 (t0) REVERT: A 84 MET cc_start: 0.8565 (mmm) cc_final: 0.8300 (mtt) REVERT: E 36 ASN cc_start: 0.8374 (t0) cc_final: 0.8048 (t0) REVERT: F 72 ASP cc_start: 0.7810 (m-30) cc_final: 0.7568 (m-30) REVERT: G 243 MET cc_start: 0.7802 (tpp) cc_final: 0.7576 (tpp) outliers start: 31 outliers final: 23 residues processed: 128 average time/residue: 0.3298 time to fit residues: 68.0205 Evaluate side-chains 130 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22726 Z= 0.262 Angle : 0.477 9.225 30855 Z= 0.253 Chirality : 0.040 0.138 3504 Planarity : 0.004 0.043 3846 Dihedral : 12.835 89.798 3694 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 11.02 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.62 (0.16), residues: 2754 helix: -0.20 (0.15), residues: 1287 sheet: 2.36 (0.25), residues: 405 loop : -1.78 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 244 PHE 0.011 0.001 PHE G 248 TYR 0.014 0.001 TYR D 315 ARG 0.008 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8451 (t0) cc_final: 0.8223 (t0) REVERT: A 84 MET cc_start: 0.8586 (mmm) cc_final: 0.8273 (mtt) REVERT: E 36 ASN cc_start: 0.8386 (t0) cc_final: 0.8123 (t0) REVERT: F 72 ASP cc_start: 0.7820 (m-30) cc_final: 0.7566 (m-30) REVERT: G 84 MET cc_start: 0.8756 (mmm) cc_final: 0.8540 (mmm) outliers start: 24 outliers final: 21 residues processed: 124 average time/residue: 0.3339 time to fit residues: 66.4655 Evaluate side-chains 130 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 198 optimal weight: 0.0770 chunk 77 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22726 Z= 0.186 Angle : 0.445 12.373 30855 Z= 0.237 Chirality : 0.039 0.144 3504 Planarity : 0.003 0.065 3846 Dihedral : 12.602 89.128 3694 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 11.20 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.51 (0.16), residues: 2754 helix: -0.12 (0.15), residues: 1296 sheet: 2.39 (0.25), residues: 405 loop : -1.71 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 244 PHE 0.009 0.001 PHE A 327 TYR 0.010 0.001 TYR C 315 ARG 0.014 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8343 (t0) cc_final: 0.8102 (t0) REVERT: A 84 MET cc_start: 0.8542 (mmm) cc_final: 0.8241 (mtt) REVERT: E 36 ASN cc_start: 0.8322 (t0) cc_final: 0.8044 (t0) REVERT: F 72 ASP cc_start: 0.7826 (m-30) cc_final: 0.7567 (m-30) REVERT: G 84 MET cc_start: 0.8701 (mmm) cc_final: 0.8492 (mmm) REVERT: G 243 MET cc_start: 0.7793 (tpp) cc_final: 0.7269 (tpp) outliers start: 25 outliers final: 23 residues processed: 127 average time/residue: 0.3519 time to fit residues: 70.4268 Evaluate side-chains 132 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22726 Z= 0.418 Angle : 0.579 10.148 30855 Z= 0.301 Chirality : 0.042 0.128 3504 Planarity : 0.004 0.058 3846 Dihedral : 13.067 86.116 3694 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.99 % Allowed : 11.42 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.73 (0.16), residues: 2754 helix: -0.26 (0.15), residues: 1296 sheet: 2.28 (0.26), residues: 396 loop : -1.83 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 244 PHE 0.017 0.002 PHE E 126 TYR 0.022 0.002 TYR D 315 ARG 0.015 0.001 ARG C 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8552 (t0) cc_final: 0.8277 (t0) REVERT: A 84 MET cc_start: 0.8519 (mmm) cc_final: 0.8293 (mtt) REVERT: E 36 ASN cc_start: 0.8407 (t0) cc_final: 0.8129 (t0) REVERT: F 72 ASP cc_start: 0.7733 (m-30) cc_final: 0.7495 (m-30) REVERT: G 84 MET cc_start: 0.8700 (mmm) cc_final: 0.8335 (mtt) REVERT: G 243 MET cc_start: 0.7901 (tpp) cc_final: 0.7400 (tpp) REVERT: I 64 LYS cc_start: 0.7566 (ptpp) cc_final: 0.7042 (mmtm) outliers start: 22 outliers final: 21 residues processed: 121 average time/residue: 0.3437 time to fit residues: 66.5603 Evaluate side-chains 130 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.052059 restraints weight = 63952.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.053613 restraints weight = 36351.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.054632 restraints weight = 25605.257| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22726 Z= 0.142 Angle : 0.424 9.676 30855 Z= 0.229 Chirality : 0.038 0.130 3504 Planarity : 0.003 0.029 3846 Dihedral : 12.500 86.829 3694 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.85 % Allowed : 11.47 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.71 (0.16), residues: 2754 helix: -0.09 (0.15), residues: 1296 sheet: 1.69 (0.27), residues: 405 loop : -1.80 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 244 PHE 0.008 0.001 PHE B 259 TYR 0.007 0.001 TYR E 301 ARG 0.003 0.000 ARG F 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.99 seconds wall clock time: 54 minutes 51.23 seconds (3291.23 seconds total)