Starting phenix.real_space_refine (version: dev) on Sat Apr 9 04:37:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jas_6353/04_2022/3jas_6353_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.028 sd= 0.918 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 411": "OE1" <-> "OE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "J GLU 434": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 411": "OE1" <-> "OE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "L GLU 434": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 345": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 40506 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.66, per 1000 atoms: 0.53 Number of scatterers: 40506 At special positions: 0 Unit cell: (170.28, 87.12, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 30 15.00 Mg 6 11.99 O 7806 8.00 N 6924 7.00 C 25464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.28 Conformation dependent library (CDL) restraints added in 5.7 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 240 helices and 36 sheets defined 48.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.628A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.098A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 4.879A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.608A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 removed outlier: 4.569A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.739A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.859A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.585A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.515A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.907A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 5.148A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 3.536A pdb=" N GLU F 393 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.109A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 435 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.628A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.593A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.099A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 4.879A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HIS J 197 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.610A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 removed outlier: 4.569A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 282 removed outlier: 3.737A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 282' Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.860A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.585A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.515A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.906A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 5.147A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 288 through 295 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 3.538A pdb=" N GLU G 393 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.108A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 435 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.629A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.098A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 4.880A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.607A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 4.571A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.737A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.858A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.590A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.515A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.907A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 5.148A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.536A pdb=" N GLU D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 4.110A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 435 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.630A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.101A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 197 removed outlier: 4.880A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS L 197 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.609A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 removed outlier: 4.570A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 282 removed outlier: 3.736A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 282' Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.860A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.500A pdb=" N TYR L 399 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.586A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.516A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.906A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 5.147A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG I 243 " --> pdb=" O THR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 288 through 295 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 3.538A pdb=" N GLU I 393 " --> pdb=" O ARG I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 4.109A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 435 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.629A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.098A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.879A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.607A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.571A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.739A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.859A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.501A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.584A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.515A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.907A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 5.149A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.537A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.111A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.629A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 197 removed outlier: 4.878A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HIS K 197 " --> pdb=" O THR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.608A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 removed outlier: 4.570A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 282 removed outlier: 3.738A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 278 through 282' Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.860A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.500A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.585A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.514A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.906A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 5.148A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 288 through 295 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.538A pdb=" N GLU H 393 " --> pdb=" O ARG H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 removed outlier: 4.109A pdb=" N GLU H 411 " --> pdb=" O TRP H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 435 Processing sheet with id= A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS E 139 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'F' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE J 5 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE J 135 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE J 7 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL J 9 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS J 139 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'G' and resid 269 through 273 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 5 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE C 135 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 7 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 9 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS C 139 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'D' and resid 269 through 273 Processing sheet with id= S, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE L 5 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE L 135 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE L 7 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL L 137 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL L 9 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS L 139 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'I' and resid 269 through 273 Processing sheet with id= Y, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.875A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= AD, first strand: chain 'B' and resid 269 through 273 Processing sheet with id= AE, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE K 5 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE K 135 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE K 7 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL K 137 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL K 9 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS K 139 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AG, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.619A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.876A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 53 through 55 Processing sheet with id= AJ, first strand: chain 'H' and resid 269 through 273 1773 hydrogen bonds defined for protein. 4662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.20 Time building geometry restraints manager: 17.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7360 1.32 - 1.45: 10850 1.45 - 1.57: 22746 1.57 - 1.69: 48 1.69 - 1.82: 432 Bond restraints: 41436 Sorted by residual: bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CA PRO E 359 " pdb=" C PRO E 359 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.86e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CA PRO J 359 " pdb=" C PRO J 359 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.75e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 95.01 - 103.40: 490 103.40 - 111.79: 16949 111.79 - 120.18: 21258 120.18 - 128.57: 17283 128.57 - 136.96: 324 Bond angle restraints: 56304 Sorted by residual: angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 111.11 117.24 -6.13 1.20e+00 6.94e-01 2.61e+01 angle pdb=" N THR C 73 " pdb=" CA THR C 73 " pdb=" C THR C 73 " ideal model delta sigma weight residual 111.11 117.22 -6.11 1.20e+00 6.94e-01 2.59e+01 angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 111.11 117.20 -6.09 1.20e+00 6.94e-01 2.58e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.17 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.16 -6.05 1.20e+00 6.94e-01 2.55e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 23795 33.72 - 67.44: 757 67.44 - 101.16: 36 101.16 - 134.87: 6 134.87 - 168.59: 18 Dihedral angle restraints: 24612 sinusoidal: 9810 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.14 -168.59 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.34 -168.39 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.54 -168.19 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3714 0.064 - 0.127: 1671 0.127 - 0.191: 580 0.191 - 0.254: 149 0.254 - 0.318: 42 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA PHE I 83 " pdb=" N PHE I 83 " pdb=" C PHE I 83 " pdb=" CB PHE I 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE F 83 " pdb=" N PHE F 83 " pdb=" C PHE F 83 " pdb=" CB PHE F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE B 83 " pdb=" N PHE B 83 " pdb=" C PHE B 83 " pdb=" CB PHE B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6153 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 288 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO F 289 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO G 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 288 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO H 289 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 289 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 289 " 0.041 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 51 2.46 - 3.07: 25490 3.07 - 3.68: 63951 3.68 - 4.29: 91498 4.29 - 4.90: 159795 Nonbonded interactions: 340785 Sorted by model distance: nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.846 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.857 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.884 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.926 2.170 ... (remaining 340780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6924 2.21 5 O 7806 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 14.100 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: 0.120 Extract box with map and model: 30.790 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.390 Process input model: 100.790 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.087 41436 Z= 0.559 Angle : 1.458 9.437 56304 Z= 1.017 Chirality : 0.083 0.318 6156 Planarity : 0.006 0.074 7338 Dihedral : 16.413 168.593 15120 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5088 helix: 1.21 (0.10), residues: 2280 sheet: 0.70 (0.19), residues: 774 loop : -0.95 (0.13), residues: 2034 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1009 time to evaluate : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 33 residues processed: 1086 average time/residue: 0.5206 time to fit residues: 913.7267 Evaluate side-chains 579 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 546 time to evaluate : 5.275 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3440 time to fit residues: 28.3859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.6980 chunk 382 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 chunk 457 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 88 HIS E 101 ASN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 91 ASN F 406 HIS J 8 HIS J 15 GLN J 35 GLN J 88 HIS J 101 ASN J 176 GLN J 266 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN G 6 HIS G 91 ASN G 349 ASN C 8 HIS C 15 GLN C 88 HIS C 101 ASN C 283 HIS D 14 ASN D 91 ASN D 349 ASN D 406 HIS L 8 HIS L 15 GLN L 88 HIS L 101 ASN L 192 HIS L 283 HIS L 300 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 91 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 349 ASN I 385 GLN I 433 GLN A 15 GLN A 18 ASN A 88 HIS A 101 ASN A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN B 14 ASN B 91 ASN B 349 ASN B 406 HIS K 8 HIS K 15 GLN K 88 HIS K 101 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN H 6 HIS H 14 ASN H 91 ASN H 349 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 41436 Z= 0.231 Angle : 0.629 8.652 56304 Z= 0.326 Chirality : 0.044 0.168 6156 Planarity : 0.006 0.080 7338 Dihedral : 12.108 173.155 5718 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 5088 helix: 1.95 (0.11), residues: 2274 sheet: 1.12 (0.18), residues: 774 loop : -0.64 (0.13), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 613 time to evaluate : 5.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 47 residues processed: 695 average time/residue: 0.5074 time to fit residues: 587.5603 Evaluate side-chains 527 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 480 time to evaluate : 4.793 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4127 time to fit residues: 42.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 380 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 458 optimal weight: 2.9990 chunk 495 optimal weight: 9.9990 chunk 408 optimal weight: 9.9990 chunk 454 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 367 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: E 11 GLN E 31 GLN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 ASN J 31 GLN J 107 HIS ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 358 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS L 31 GLN L 88 HIS L 358 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 309 HIS I 350 ASN I 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 37 HIS ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 107 HIS ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 358 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN H 337 ASN H 350 ASN H 406 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 41436 Z= 0.351 Angle : 0.623 7.825 56304 Z= 0.323 Chirality : 0.045 0.165 6156 Planarity : 0.005 0.076 7338 Dihedral : 11.870 176.722 5718 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 5088 helix: 1.65 (0.11), residues: 2268 sheet: 1.35 (0.18), residues: 792 loop : -0.83 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 531 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 47 residues processed: 616 average time/residue: 0.5022 time to fit residues: 518.0062 Evaluate side-chains 498 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 451 time to evaluate : 4.799 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4168 time to fit residues: 42.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 0.9990 chunk 344 optimal weight: 0.7980 chunk 237 optimal weight: 0.0070 chunk 50 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 307 optimal weight: 10.0000 chunk 460 optimal weight: 0.8980 chunk 487 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 436 optimal weight: 0.0870 chunk 131 optimal weight: 6.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN F 14 ASN J 300 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 ASN C 11 GLN C 31 GLN D 11 GLN D 136 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN B 11 GLN B 14 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS H 229 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 41436 Z= 0.153 Angle : 0.539 8.913 56304 Z= 0.274 Chirality : 0.041 0.176 6156 Planarity : 0.005 0.090 7338 Dihedral : 11.520 179.269 5718 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 5088 helix: 1.80 (0.11), residues: 2280 sheet: 1.40 (0.18), residues: 792 loop : -0.74 (0.13), residues: 2016 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 565 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 25 residues processed: 613 average time/residue: 0.4926 time to fit residues: 505.3777 Evaluate side-chains 493 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 468 time to evaluate : 4.968 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3664 time to fit residues: 23.7459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 415 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 437 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 300 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 HIS G 339 ASN C 11 GLN D 336 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS A 101 ASN B 14 ASN B 193 GLN B 206 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 41436 Z= 0.202 Angle : 0.537 9.771 56304 Z= 0.273 Chirality : 0.042 0.145 6156 Planarity : 0.005 0.087 7338 Dihedral : 11.337 179.168 5718 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 5088 helix: 1.74 (0.11), residues: 2286 sheet: 1.59 (0.18), residues: 762 loop : -0.70 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 495 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 542 average time/residue: 0.4985 time to fit residues: 455.3355 Evaluate side-chains 486 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 451 time to evaluate : 4.921 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3825 time to fit residues: 32.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 1.9990 chunk 438 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 487 optimal weight: 1.9990 chunk 404 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 HIS E 256 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 HIS G 339 ASN D 206 ASN D 337 ASN L 107 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 337 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 41436 Z= 0.308 Angle : 0.574 10.525 56304 Z= 0.293 Chirality : 0.044 0.156 6156 Planarity : 0.005 0.084 7338 Dihedral : 11.340 177.588 5718 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 5088 helix: 1.68 (0.11), residues: 2244 sheet: 1.52 (0.19), residues: 762 loop : -0.71 (0.13), residues: 2082 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 494 time to evaluate : 5.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 533 average time/residue: 0.5180 time to fit residues: 465.5701 Evaluate side-chains 482 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 453 time to evaluate : 5.238 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3797 time to fit residues: 27.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 277 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 485 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN F 136 GLN F 206 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 41436 Z= 0.173 Angle : 0.531 11.929 56304 Z= 0.269 Chirality : 0.041 0.150 6156 Planarity : 0.005 0.087 7338 Dihedral : 11.102 177.900 5718 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.12), residues: 5088 helix: 1.79 (0.11), residues: 2232 sheet: 1.63 (0.19), residues: 756 loop : -0.75 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 513 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 535 average time/residue: 0.5015 time to fit residues: 449.1854 Evaluate side-chains 475 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 455 time to evaluate : 4.799 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3509 time to fit residues: 19.7459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 8.9990 chunk 193 optimal weight: 0.2980 chunk 290 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 381 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS B 193 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 41436 Z= 0.181 Angle : 0.541 12.610 56304 Z= 0.272 Chirality : 0.042 0.145 6156 Planarity : 0.005 0.091 7338 Dihedral : 10.972 178.159 5718 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.12), residues: 5088 helix: 1.70 (0.11), residues: 2268 sheet: 1.64 (0.19), residues: 756 loop : -0.71 (0.14), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 482 time to evaluate : 4.887 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 498 average time/residue: 0.5104 time to fit residues: 427.1113 Evaluate side-chains 467 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 457 time to evaluate : 4.864 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4053 time to fit residues: 14.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 4.9990 chunk 465 optimal weight: 0.9990 chunk 424 optimal weight: 0.9990 chunk 452 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 355 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 409 optimal weight: 0.4980 chunk 428 optimal weight: 7.9990 chunk 451 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN F 349 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 192 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 41436 Z= 0.171 Angle : 0.532 13.034 56304 Z= 0.268 Chirality : 0.041 0.191 6156 Planarity : 0.004 0.094 7338 Dihedral : 10.748 177.087 5718 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.12), residues: 5088 helix: 1.63 (0.11), residues: 2304 sheet: 1.64 (0.19), residues: 756 loop : -0.75 (0.14), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 481 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 491 average time/residue: 0.5193 time to fit residues: 427.7015 Evaluate side-chains 466 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 453 time to evaluate : 5.268 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3651 time to fit residues: 15.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 0.7980 chunk 478 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 227 optimal weight: 0.0970 chunk 332 optimal weight: 0.9980 chunk 502 optimal weight: 7.9990 chunk 462 optimal weight: 6.9990 chunk 399 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 245 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN F 192 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 HIS G 433 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.090 41436 Z= 0.158 Angle : 0.537 13.492 56304 Z= 0.269 Chirality : 0.041 0.167 6156 Planarity : 0.004 0.102 7338 Dihedral : 10.539 179.332 5718 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 5088 helix: 1.63 (0.11), residues: 2310 sheet: 1.69 (0.19), residues: 798 loop : -0.68 (0.14), residues: 1980 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 498 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 503 average time/residue: 0.5227 time to fit residues: 445.9421 Evaluate side-chains 467 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 464 time to evaluate : 4.776 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3698 time to fit residues: 8.4799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 6.9990 chunk 425 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 368 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 400 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 411 optimal weight: 3.9990 chunk 50 optimal weight: 0.0010 chunk 73 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN J 101 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087049 restraints weight = 67200.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090460 restraints weight = 32398.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092785 restraints weight = 19437.656| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 41436 Z= 0.155 Angle : 0.538 13.469 56304 Z= 0.268 Chirality : 0.041 0.153 6156 Planarity : 0.004 0.097 7338 Dihedral : 10.340 178.598 5718 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 5088 helix: 1.68 (0.11), residues: 2298 sheet: 1.70 (0.19), residues: 798 loop : -0.71 (0.14), residues: 1992 =============================================================================== Job complete usr+sys time: 8869.27 seconds wall clock time: 162 minutes 24.57 seconds (9744.57 seconds total)