Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 15:27:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/05_2023/6qg0_4543_updated.pdb" } resolution = 4.15 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= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 162 5.16 5 C 23526 2.51 5 N 6322 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G GLU 508": "OE1" <-> "OE2" Residue "G GLU 538": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H GLU 436": "OE1" <-> "OE2" Residue "H GLU 508": "OE1" <-> "OE2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H GLU 583": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 370": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "M GLU 506": "OE1" <-> "OE2" Residue "N GLU 231": "OE1" <-> "OE2" Residue "N PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 506": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 93": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36980 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 17.32, per 1000 atoms: 0.47 Number of scatterers: 36980 At special positions: 0 Unit cell: (274.7, 167.5, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 P 2 15.00 O 6968 8.00 N 6322 7.00 C 23526 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: 12.32 Conformation dependent library (CDL) restraints added in 5.0 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 48 sheets defined 29.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.917A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.639A pdb=" N ASP A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.546A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.514A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.520A pdb=" N VAL A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.788A pdb=" N THR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.649A pdb=" N ASP B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 115 removed outlier: 4.257A pdb=" N GLY B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.534A pdb=" N VAL B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 82 through 107 removed outlier: 3.550A pdb=" N ILE D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'D' and resid 169 through 176 removed outlier: 3.993A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.119A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.992A pdb=" N GLN E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 287 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 288 " --> pdb=" O CYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 411 removed outlier: 3.533A pdb=" N ASN E 405 " --> pdb=" O MET E 402 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 409 " --> pdb=" O ARG E 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 411 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 282 through 288 removed outlier: 3.997A pdb=" N GLN F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 287 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 288 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 411 removed outlier: 3.559A pdb=" N ASN F 405 " --> pdb=" O MET F 402 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE F 407 " --> pdb=" O ALA F 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 411 " --> pdb=" O VAL F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 removed outlier: 4.054A pdb=" N HIS G 283 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 306 removed outlier: 3.904A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 338 through 353 Processing helix chain 'G' and resid 360 through 378 removed outlier: 3.704A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 393 removed outlier: 3.743A pdb=" N GLN G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 418 Processing helix chain 'G' and resid 436 through 447 Processing helix chain 'G' and resid 490 through 498 Processing helix chain 'G' and resid 529 through 532 Processing helix chain 'H' and resid 272 through 283 removed outlier: 4.048A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 306 removed outlier: 3.723A pdb=" N ILE H 294 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 338 through 353 Processing helix chain 'H' and resid 360 through 378 removed outlier: 3.541A pdb=" N LYS H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 393 removed outlier: 3.623A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 417 Processing helix chain 'H' and resid 436 through 447 Processing helix chain 'H' and resid 456 through 462 removed outlier: 3.571A pdb=" N LEU H 459 " --> pdb=" O ILE H 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP H 460 " --> pdb=" O THR H 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H 461 " --> pdb=" O SER H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'H' and resid 529 through 532 Processing helix chain 'H' and resid 583 through 588 removed outlier: 6.039A pdb=" N LYS H 587 " --> pdb=" O GLY H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 83 through 91 Processing helix chain 'I' and resid 115 through 125 Processing helix chain 'I' and resid 146 through 156 Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 241 through 248 Processing helix chain 'I' and resid 259 through 264 Processing helix chain 'I' and resid 288 through 299 Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'J' and resid 59 through 70 removed outlier: 3.515A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 91 Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 146 through 156 Processing helix chain 'J' and resid 215 through 221 removed outlier: 4.175A pdb=" N LEU J 218 " --> pdb=" O PRO J 215 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP J 219 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN J 220 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 221 " --> pdb=" O LEU J 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 215 through 221' Processing helix chain 'J' and resid 241 through 248 Processing helix chain 'J' and resid 259 through 264 Processing helix chain 'J' and resid 288 through 299 Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'L' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 141 through 150 removed outlier: 3.731A pdb=" N ILE L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 173 Processing helix chain 'L' and resid 198 through 208 Processing helix chain 'L' and resid 238 through 258 removed outlier: 3.545A pdb=" N ILE L 241 " --> pdb=" O GLN L 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU L 242 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 243 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU L 244 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU L 245 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 246 " --> pdb=" O GLN L 243 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 248 " --> pdb=" O GLU L 245 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS L 250 " --> pdb=" O ALA L 247 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 252 " --> pdb=" O GLU L 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 253 " --> pdb=" O LYS L 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 255 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR L 258 " --> pdb=" O ILE L 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 120 Processing helix chain 'M' and resid 202 through 210 removed outlier: 3.592A pdb=" N ALA M 209 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 238 Processing helix chain 'M' and resid 258 through 269 Processing helix chain 'M' and resid 291 through 301 removed outlier: 3.602A pdb=" N VAL M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'N' and resid 113 through 120 Processing helix chain 'N' and resid 202 through 210 removed outlier: 3.570A pdb=" N ALA N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 238 Processing helix chain 'N' and resid 256 through 269 removed outlier: 3.821A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 301 removed outlier: 3.566A pdb=" N VAL N 299 " --> pdb=" O ASN N 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 140 Processing helix chain 'K' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 141 through 150 removed outlier: 3.747A pdb=" N ILE K 150 " --> pdb=" O LYS K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'K' and resid 198 through 208 Processing helix chain 'K' and resid 238 through 258 removed outlier: 3.535A pdb=" N ILE K 241 " --> pdb=" O GLN K 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 242 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 243 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU K 245 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 246 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K 248 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 250 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR K 252 " --> pdb=" O GLU K 249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU K 253 " --> pdb=" O LYS K 250 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE K 255 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 257 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 258 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 61 through 77 Processing helix chain 'C' and resid 82 through 107 removed outlier: 3.548A pdb=" N ILE C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 169 through 176 removed outlier: 3.992A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 309 through 312 No H-bonds generated for 'chain 'C' and resid 309 through 312' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 361 through 366 Processing sheet with id= A, first strand: chain 'A' and resid 282 through 284 removed outlier: 7.389A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 209 Processing sheet with id= C, first strand: chain 'B' and resid 282 through 284 removed outlier: 3.637A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR B 177 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.516A pdb=" N ASN B 209 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 348 through 350 removed outlier: 3.964A pdb=" N ILE D 348 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY D 261 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 339 through 341 removed outlier: 3.638A pdb=" N ASP D 339 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 133 through 137 removed outlier: 7.685A pdb=" N ILE E 92 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLN E 136 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 94 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 194 through 199 Processing sheet with id= I, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= J, first strand: chain 'F' and resid 133 through 137 removed outlier: 7.603A pdb=" N ILE F 92 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLN F 136 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 94 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 194 through 199 Processing sheet with id= L, first strand: chain 'F' and resid 223 through 225 Processing sheet with id= M, first strand: chain 'G' and resid 579 through 581 removed outlier: 8.045A pdb=" N VAL G 503 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN G 574 " --> pdb=" O VAL G 503 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 505 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE G 576 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL G 470 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS G 506 " --> pdb=" O VAL G 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 472 " --> pdb=" O CYS G 506 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR G 403 " --> pdb=" O PHE G 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 473 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS G 425 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR G 402 " --> pdb=" O LYS G 425 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE G 427 " --> pdb=" O THR G 402 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 564 through 566 Processing sheet with id= O, first strand: chain 'H' and resid 571 through 575 removed outlier: 7.660A pdb=" N VAL H 503 " --> pdb=" O LYS H 572 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN H 574 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 505 " --> pdb=" O ASN H 574 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL H 470 " --> pdb=" O LEU H 504 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 506 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 472 " --> pdb=" O CYS H 506 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR H 403 " --> pdb=" O PHE H 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 473 " --> pdb=" O TYR H 403 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS H 425 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR H 402 " --> pdb=" O LYS H 425 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 427 " --> pdb=" O THR H 402 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 564 through 566 Processing sheet with id= Q, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.509A pdb=" N ILE I 237 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN I 28 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL I 135 " --> pdb=" O GLN I 28 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL I 30 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU I 74 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 31 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE I 76 " --> pdb=" O VAL I 31 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS I 103 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU I 77 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR I 105 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS I 79 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 107 " --> pdb=" O CYS I 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 139 through 141 removed outlier: 4.039A pdb=" N LEU I 140 " --> pdb=" O VAL I 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL I 283 " --> pdb=" O LEU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 276 through 278 removed outlier: 3.594A pdb=" N LYS I 170 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 224 through 227 removed outlier: 3.635A pdb=" N GLN I 198 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 186 " --> pdb=" O TYR I 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 196 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP I 188 " --> pdb=" O CYS I 194 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS I 194 " --> pdb=" O ASP I 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.441A pdb=" N THR I 343 " --> pdb=" O TYR I 326 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 331 through 333 removed outlier: 5.804A pdb=" N THR I 349 " --> pdb=" O VAL I 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'I' and resid 356 through 358 Processing sheet with id= X, first strand: chain 'I' and resid 394 through 396 removed outlier: 6.255A pdb=" N CYS I 412 " --> pdb=" O LEU I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.510A pdb=" N ILE J 237 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN J 28 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N VAL J 135 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL J 30 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU J 74 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL J 31 " --> pdb=" O GLU J 74 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE J 76 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS J 103 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU J 77 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR J 105 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS J 79 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE J 107 " --> pdb=" O CYS J 79 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 139 through 141 removed outlier: 4.052A pdb=" N LEU J 140 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL J 283 " --> pdb=" O LEU J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'J' and resid 276 through 278 removed outlier: 3.517A pdb=" N LYS J 170 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 169 " --> pdb=" O ILE J 231 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 185 through 188 Processing sheet with id= AC, first strand: chain 'J' and resid 319 through 321 removed outlier: 6.435A pdb=" N THR J 343 " --> pdb=" O TYR J 326 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 331 through 333 removed outlier: 5.788A pdb=" N THR J 349 " --> pdb=" O VAL J 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 356 through 358 Processing sheet with id= AF, first strand: chain 'J' and resid 394 through 396 removed outlier: 6.229A pdb=" N CYS J 412 " --> pdb=" O LEU J 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'L' and resid 262 through 264 Processing sheet with id= AH, first strand: chain 'L' and resid 72 through 77 removed outlier: 6.628A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 280 through 282 removed outlier: 8.636A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE M 101 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER M 190 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR M 105 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL M 186 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE M 147 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS M 188 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA M 145 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 143 " --> pdb=" O SER M 190 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 373 through 376 removed outlier: 4.352A pdb=" N ASN M 344 " --> pdb=" O ARG M 314 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE M 316 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE M 342 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE M 342 " --> pdb=" O GLY M 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 319 through 321 Processing sheet with id= AL, first strand: chain 'M' and resid 425 through 427 removed outlier: 3.756A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 482 through 486 removed outlier: 7.248A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 280 through 282 removed outlier: 8.591A pdb=" N VAL N 281 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 246 " --> pdb=" O VAL N 281 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA N 214 " --> pdb=" O ILE N 245 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU N 247 " --> pdb=" O ALA N 214 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU N 216 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE N 101 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER N 190 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR N 105 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL N 186 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE N 147 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS N 188 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA N 145 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER N 190 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA N 143 " --> pdb=" O SER N 190 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 373 through 376 removed outlier: 4.336A pdb=" N ASN N 344 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE N 316 " --> pdb=" O ILE N 342 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE N 342 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE N 342 " --> pdb=" O GLY N 394 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY N 394 " --> pdb=" O ILE N 342 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 319 through 321 Processing sheet with id= AQ, first strand: chain 'N' and resid 425 through 427 removed outlier: 3.710A pdb=" N ASN N 425 " --> pdb=" O THR N 493 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 482 through 486 removed outlier: 7.259A pdb=" N LEU N 501 " --> pdb=" O ILE N 512 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP N 514 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE N 499 " --> pdb=" O TRP N 514 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG N 504 " --> pdb=" O VAL N 461 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL N 461 " --> pdb=" O ARG N 504 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 484 " --> pdb=" O VAL N 476 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'K' and resid 262 through 264 Processing sheet with id= AT, first strand: chain 'K' and resid 72 through 77 removed outlier: 6.629A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.965A pdb=" N ILE C 348 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 261 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 339 through 341 removed outlier: 3.636A pdb=" N ASP C 339 " --> pdb=" O SER C 273 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3096 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: 11.39 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6299 1.32 - 1.45: 9109 1.45 - 1.57: 21943 1.57 - 1.70: 5 1.70 - 1.83: 242 Bond restraints: 37598 Sorted by residual: bond pdb=" N ASN B 89 " pdb=" CA ASN B 89 " ideal model delta sigma weight residual 1.459 1.543 -0.085 1.28e-02 6.10e+03 4.37e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.495 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C ALA B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.334 1.254 0.080 1.42e-02 4.96e+03 3.21e+01 bond pdb=" O1P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 37593 not shown) Histogram of bond angle deviations from ideal: 96.44 - 103.99: 483 103.99 - 111.55: 13726 111.55 - 119.10: 16842 119.10 - 126.65: 19489 126.65 - 134.21: 350 Bond angle restraints: 50890 Sorted by residual: angle pdb=" N ARG N 356 " pdb=" CA ARG N 356 " pdb=" C ARG N 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ARG M 356 " pdb=" CA ARG M 356 " pdb=" C ARG M 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ILE H 501 " pdb=" CA ILE H 501 " pdb=" C ILE H 501 " ideal model delta sigma weight residual 109.02 114.80 -5.78 9.30e-01 1.16e+00 3.86e+01 angle pdb=" CA LEU C 125 " pdb=" C LEU C 125 " pdb=" N GLN C 126 " ideal model delta sigma weight residual 119.56 116.25 3.31 5.80e-01 2.97e+00 3.25e+01 angle pdb=" N ILE A 207 " pdb=" CA ILE A 207 " pdb=" C ILE A 207 " ideal model delta sigma weight residual 108.46 116.34 -7.88 1.49e+00 4.50e-01 2.79e+01 ... (remaining 50885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 19287 16.66 - 33.32: 2680 33.32 - 49.98: 612 49.98 - 66.63: 334 66.63 - 83.29: 69 Dihedral angle restraints: 22982 sinusoidal: 9164 harmonic: 13818 Sorted by residual: dihedral pdb=" C GLN I 289 " pdb=" N GLN I 289 " pdb=" CA GLN I 289 " pdb=" CB GLN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.49 13.89 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" C LEU J 202 " pdb=" N LEU J 202 " pdb=" CA LEU J 202 " pdb=" CB LEU J 202 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLN J 289 " pdb=" N GLN J 289 " pdb=" CA GLN J 289 " pdb=" CB GLN J 289 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 22979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5051 0.109 - 0.217: 800 0.217 - 0.326: 98 0.326 - 0.434: 15 0.434 - 0.543: 8 Chirality restraints: 5972 Sorted by residual: chirality pdb=" CA GLN I 289 " pdb=" N GLN I 289 " pdb=" C GLN I 289 " pdb=" CB GLN I 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA GLN J 289 " pdb=" N GLN J 289 " pdb=" C GLN J 289 " pdb=" CB GLN J 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 5969 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 51 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU L 51 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU L 51 " 0.022 2.00e-02 2.50e+03 pdb=" N SEP L 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 249 " -0.016 2.00e-02 2.50e+03 2.35e-02 9.66e+00 pdb=" CG PHE C 249 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE C 249 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 249 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 249 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 249 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 24 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C VAL K 24 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL K 24 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN K 25 " 0.018 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.60: 6 1.60 - 2.42: 17 2.42 - 3.25: 31767 3.25 - 4.07: 88855 4.07 - 4.90: 152385 Warning: very small nonbonded interaction distances. Nonbonded interactions: 273030 Sorted by model distance: nonbonded pdb=" NE2 GLN L 26 " pdb=" CB ALA L 32 " model vdw 0.775 3.540 nonbonded pdb=" NE2 GLN L 26 " pdb=" CA ALA L 32 " model vdw 0.867 3.550 nonbonded pdb=" CD GLN L 26 " pdb=" CA ALA L 32 " model vdw 1.219 3.700 nonbonded pdb=" ND2 ASN A 80 " pdb=" CD2 LEU A 94 " model vdw 1.552 3.540 nonbonded pdb=" ND2 ASN B 80 " pdb=" CG LEU B 94 " model vdw 1.572 3.550 ... (remaining 273025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.160 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 79.870 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.115 37598 Z= 0.589 Angle : 1.399 12.373 50890 Z= 0.896 Chirality : 0.083 0.543 5972 Planarity : 0.005 0.047 6496 Dihedral : 18.074 83.294 13990 Min Nonbonded Distance : 0.775 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.97 % Favored : 87.59 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.10), residues: 4632 helix: -2.05 (0.10), residues: 1536 sheet: -0.65 (0.19), residues: 606 loop : -2.53 (0.11), residues: 2490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1183 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 241 outliers final: 54 residues processed: 1337 average time/residue: 0.4811 time to fit residues: 1030.6774 Evaluate side-chains 748 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 694 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3314 time to fit residues: 35.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 423 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 144 ASN A 164 GLN A 222 ASN B 62 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN D 10 HIS D 72 ASN D 221 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 14 ASN E 59 GLN E 308 ASN E 309 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN G 280 HIS G 301 GLN G 384 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN H 384 GLN ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 539 ASN H 546 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 HIS I 247 GLN I 296 GLN I 429 ASN J 247 GLN J 296 GLN J 371 ASN J 409 ASN L 103 GLN M 98 GLN M 108 HIS M 197 HIS M 286 GLN N 197 HIS N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN K 243 GLN C 10 HIS C 61 ASN C 72 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 37598 Z= 0.245 Angle : 0.737 14.196 50890 Z= 0.384 Chirality : 0.048 0.418 5972 Planarity : 0.005 0.081 6496 Dihedral : 5.919 81.289 5048 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 1.06 % Allowed : 8.57 % Favored : 90.37 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.11), residues: 4632 helix: -0.17 (0.12), residues: 1548 sheet: 0.01 (0.20), residues: 586 loop : -2.41 (0.11), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 881 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 16 outliers final: 2 residues processed: 892 average time/residue: 0.4514 time to fit residues: 663.8890 Evaluate side-chains 636 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 634 time to evaluate : 3.284 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2806 time to fit residues: 5.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 3.9990 chunk 131 optimal weight: 0.0050 chunk 352 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 116 optimal weight: 0.0040 chunk 423 optimal weight: 30.0000 chunk 457 optimal weight: 0.8980 chunk 377 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 overall best weight: 1.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: