Starting phenix.real_space_refine on Tue Apr 16 17:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/04_2024/7yk5_33887_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 16 5.49 5 S 248 5.16 5 C 25288 2.51 5 N 6844 2.21 5 O 7552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 253": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 112": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39948 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'CSO:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1, 'HLU:plan-1': 1, 'HYP:plan-1': 2, 'LYO:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "J" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "K" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "L" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "M" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "O" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "P" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "h" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "g" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "f" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "e" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "d" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "c" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "b" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "a" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.37, per 1000 atoms: 0.48 Number of scatterers: 39948 At special positions: 0 Unit cell: (136.422, 136.422, 132.99, 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 248 16.00 P 16 15.00 O 7552 8.00 N 6844 7.00 C 25288 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: 16.56 Conformation dependent library (CDL) restraints added in 6.2 seconds 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 40 sheets defined 35.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 84 No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 218 through 236 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.955A pdb=" N ALA A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 387 through 397 removed outlier: 5.390A pdb=" N HIS A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 394 " --> pdb=" O HIS A 391 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 445 through 456 removed outlier: 4.385A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'B' and resid 5 through 8 No H-bonds generated for 'chain 'B' and resid 5 through 8' Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 81 through 84 No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 218 through 236 Processing helix chain 'B' and resid 251 through 264 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 277 through 290 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.957A pdb=" N ALA B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 387 through 397 removed outlier: 5.390A pdb=" N HIS B 391 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 394 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 397 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 410 No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 416 through 436 Processing helix chain 'B' and resid 445 through 456 removed outlier: 4.347A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 54 through 64 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 81 through 84 No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 186 through 199 Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 251 through 264 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 277 through 290 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.955A pdb=" N ALA C 305 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 324 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 387 through 397 removed outlier: 5.389A pdb=" N HIS C 391 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 394 " --> pdb=" O HIS C 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 397 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 416 through 436 Processing helix chain 'C' and resid 445 through 456 removed outlier: 4.349A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'D' and resid 5 through 8 No H-bonds generated for 'chain 'D' and resid 5 through 8' Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 81 through 84 No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 159 through 166 Processing helix chain 'D' and resid 186 through 199 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 277 through 290 Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.957A pdb=" N ALA D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 324 Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 387 through 397 removed outlier: 5.389A pdb=" N HIS D 391 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 394 " --> pdb=" O HIS D 391 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 397 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 410 No H-bonds generated for 'chain 'D' and resid 407 through 410' Processing helix chain 'D' and resid 416 through 436 Processing helix chain 'D' and resid 445 through 456 removed outlier: 4.354A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'E' and resid 5 through 8 No H-bonds generated for 'chain 'E' and resid 5 through 8' Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 54 through 64 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 81 through 84 No H-bonds generated for 'chain 'E' and resid 81 through 84' Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 186 through 199 Processing helix chain 'E' and resid 218 through 236 Processing helix chain 'E' and resid 251 through 263 Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 277 through 290 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.955A pdb=" N ALA E 305 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 324 Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 387 through 397 removed outlier: 5.389A pdb=" N HIS E 391 " --> pdb=" O GLY E 388 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 394 " --> pdb=" O HIS E 391 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 397 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 410 No H-bonds generated for 'chain 'E' and resid 407 through 410' Processing helix chain 'E' and resid 416 through 436 Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.354A pdb=" N THR E 456 " --> pdb=" O ASN E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'F' and resid 5 through 8 No H-bonds generated for 'chain 'F' and resid 5 through 8' Processing helix chain 'F' and resid 23 through 25 No H-bonds generated for 'chain 'F' and resid 23 through 25' Processing helix chain 'F' and resid 54 through 64 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 81 through 84 No H-bonds generated for 'chain 'F' and resid 81 through 84' Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 186 through 199 Processing helix chain 'F' and resid 218 through 236 Processing helix chain 'F' and resid 251 through 263 Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 277 through 290 Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.957A pdb=" N ALA F 305 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 324 Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 387 through 397 removed outlier: 5.390A pdb=" N HIS F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 394 " --> pdb=" O HIS F 391 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU F 397 " --> pdb=" O VAL F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 416 through 436 Processing helix chain 'F' and resid 445 through 456 removed outlier: 4.370A pdb=" N THR F 456 " --> pdb=" O ASN F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 466 Processing helix chain 'G' and resid 5 through 8 No H-bonds generated for 'chain 'G' and resid 5 through 8' Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 54 through 64 Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 81 through 84 No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 117 through 124 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 186 through 199 Processing helix chain 'G' and resid 218 through 236 Processing helix chain 'G' and resid 251 through 263 Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 277 through 290 Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.955A pdb=" N ALA G 305 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 324 Processing helix chain 'G' and resid 344 through 353 Processing helix chain 'G' and resid 361 through 363 No H-bonds generated for 'chain 'G' and resid 361 through 363' Processing helix chain 'G' and resid 387 through 397 removed outlier: 5.391A pdb=" N HIS G 391 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL G 394 " --> pdb=" O HIS G 391 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU G 397 " --> pdb=" O VAL G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 410 No H-bonds generated for 'chain 'G' and resid 407 through 410' Processing helix chain 'G' and resid 416 through 436 Processing helix chain 'G' and resid 445 through 456 removed outlier: 4.369A pdb=" N THR G 456 " --> pdb=" O ASN G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 466 Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 23 through 25 No H-bonds generated for 'chain 'H' and resid 23 through 25' Processing helix chain 'H' and resid 54 through 64 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 81 through 84 No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 117 through 124 Processing helix chain 'H' and resid 128 through 130 No H-bonds generated for 'chain 'H' and resid 128 through 130' Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 186 through 199 Processing helix chain 'H' and resid 218 through 236 Processing helix chain 'H' and resid 251 through 263 Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 277 through 290 Processing helix chain 'H' and resid 301 through 305 removed outlier: 3.957A pdb=" N ALA H 305 " --> pdb=" O SER H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 344 through 353 Processing helix chain 'H' and resid 361 through 363 No H-bonds generated for 'chain 'H' and resid 361 through 363' Processing helix chain 'H' and resid 387 through 397 removed outlier: 5.390A pdb=" N HIS H 391 " --> pdb=" O GLY H 388 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 394 " --> pdb=" O HIS H 391 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU H 397 " --> pdb=" O VAL H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 410 No H-bonds generated for 'chain 'H' and resid 407 through 410' Processing helix chain 'H' and resid 416 through 436 Processing helix chain 'H' and resid 445 through 456 removed outlier: 4.385A pdb=" N THR H 456 " --> pdb=" O ASN H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 458 through 466 Processing helix chain 'I' and resid 16 through 28 Processing helix chain 'I' and resid 61 through 74 Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 61 through 74 Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'K' and resid 16 through 28 Processing helix chain 'K' and resid 61 through 74 Processing helix chain 'K' and resid 128 through 132 Processing helix chain 'L' and resid 16 through 28 Processing helix chain 'L' and resid 61 through 74 Processing helix chain 'L' and resid 128 through 132 Processing helix chain 'M' and resid 16 through 28 Processing helix chain 'M' and resid 61 through 74 Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'N' and resid 16 through 28 Processing helix chain 'N' and resid 61 through 74 Processing helix chain 'N' and resid 128 through 132 Processing helix chain 'O' and resid 16 through 28 Processing helix chain 'O' and resid 61 through 74 Processing helix chain 'O' and resid 128 through 132 Processing helix chain 'P' and resid 16 through 28 Processing helix chain 'P' and resid 61 through 74 Processing helix chain 'P' and resid 128 through 132 Processing sheet with id= A, first strand: chain 'A' and resid 136 through 143 removed outlier: 3.754A pdb=" N ALA A 136 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 43 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A 142 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 41 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 90 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 106 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA A 88 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 268 through 272 removed outlier: 6.186A pdb=" N ILE A 293 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE A 271 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 295 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.457A pdb=" N MET A 378 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 136 through 143 removed outlier: 3.752A pdb=" N ALA B 136 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 43 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET B 142 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 41 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B 90 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 106 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA B 88 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 268 through 272 removed outlier: 6.186A pdb=" N ILE B 293 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE B 271 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS B 295 " --> pdb=" O ILE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.456A pdb=" N MET B 378 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 136 through 143 removed outlier: 3.755A pdb=" N ALA C 136 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 43 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET C 142 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 41 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 90 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA C 106 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA C 88 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 268 through 272 removed outlier: 6.186A pdb=" N ILE C 293 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 271 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS C 295 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.453A pdb=" N MET C 378 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 136 through 143 removed outlier: 3.754A pdb=" N ALA D 136 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D 43 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET D 142 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 41 " --> pdb=" O MET D 142 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 90 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA D 106 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA D 88 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 268 through 272 removed outlier: 6.186A pdb=" N ILE D 293 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE D 271 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS D 295 " --> pdb=" O ILE D 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.455A pdb=" N MET D 378 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 136 through 143 removed outlier: 3.753A pdb=" N ALA E 136 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 43 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET E 142 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 41 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 90 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA E 106 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA E 88 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 268 through 272 removed outlier: 6.187A pdb=" N ILE E 293 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE E 271 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS E 295 " --> pdb=" O ILE E 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.456A pdb=" N MET E 378 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 136 through 143 removed outlier: 3.754A pdb=" N ALA F 136 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU F 43 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET F 142 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU F 41 " --> pdb=" O MET F 142 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 90 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA F 106 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA F 88 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 268 through 272 removed outlier: 6.186A pdb=" N ILE F 293 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE F 271 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS F 295 " --> pdb=" O ILE F 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.456A pdb=" N MET F 378 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 136 through 143 removed outlier: 3.753A pdb=" N ALA G 136 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU G 43 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET G 142 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU G 41 " --> pdb=" O MET G 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG G 90 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA G 106 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ALA G 88 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 268 through 272 removed outlier: 6.185A pdb=" N ILE G 293 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE G 271 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS G 295 " --> pdb=" O ILE G 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.456A pdb=" N MET G 378 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 136 through 143 removed outlier: 3.756A pdb=" N ALA H 136 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU H 43 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET H 142 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU H 41 " --> pdb=" O MET H 142 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 90 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA H 106 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA H 88 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 268 through 272 removed outlier: 6.187A pdb=" N ILE H 293 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE H 271 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS H 295 " --> pdb=" O ILE H 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.457A pdb=" N MET H 378 " --> pdb=" O ILE H 329 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.608A pdb=" N ASN I 101 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE I 82 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE I 99 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA I 84 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER I 97 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 109 through 115 Processing sheet with id= AA, first strand: chain 'J' and resid 32 through 38 removed outlier: 3.614A pdb=" N ASN J 101 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE J 82 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE J 99 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA J 84 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER J 97 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 109 through 115 Processing sheet with id= AC, first strand: chain 'K' and resid 32 through 38 removed outlier: 3.592A pdb=" N ASN K 101 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE K 82 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE K 99 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA K 84 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER K 97 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 109 through 115 Processing sheet with id= AE, first strand: chain 'L' and resid 32 through 38 removed outlier: 3.611A pdb=" N ASN L 101 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE L 82 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE L 99 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA L 84 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER L 97 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 109 through 115 Processing sheet with id= AG, first strand: chain 'M' and resid 32 through 38 removed outlier: 3.612A pdb=" N ASN M 101 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE M 82 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ILE M 99 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA M 84 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER M 97 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 109 through 115 Processing sheet with id= AI, first strand: chain 'N' and resid 32 through 38 removed outlier: 3.615A pdb=" N ASN N 101 " --> pdb=" O ILE N 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE N 82 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE N 99 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA N 84 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER N 97 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 109 through 115 Processing sheet with id= AK, first strand: chain 'O' and resid 32 through 38 removed outlier: 3.612A pdb=" N ASN O 101 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE O 82 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE O 99 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA O 84 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER O 97 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 109 through 115 Processing sheet with id= AM, first strand: chain 'P' and resid 32 through 38 removed outlier: 3.615A pdb=" N ASN P 101 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE P 82 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE P 99 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA P 84 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER P 97 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 109 through 115 1306 hydrogen bonds defined for protein. 3462 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: 15.37 Time building geometry restraints manager: 17.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7988 1.33 - 1.46: 10246 1.46 - 1.58: 22218 1.58 - 1.70: 24 1.70 - 1.83: 400 Bond restraints: 40876 Sorted by residual: bond pdb=" N GLN C 213 " pdb=" CA GLN C 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.65e+01 bond pdb=" N GLN A 213 " pdb=" CA GLN A 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.65e+01 bond pdb=" N GLN E 213 " pdb=" CA GLN E 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.61e+01 bond pdb=" N GLN H 213 " pdb=" CA GLN H 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.58e+01 bond pdb=" N GLN D 213 " pdb=" CA GLN D 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.58e+01 ... (remaining 40871 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.89: 1315 106.89 - 113.77: 21580 113.77 - 120.64: 18778 120.64 - 127.52: 13467 127.52 - 134.39: 344 Bond angle restraints: 55484 Sorted by residual: angle pdb=" CA GLY P 6 " pdb=" C GLY P 6 " pdb=" O GLY P 6 " ideal model delta sigma weight residual 122.45 117.96 4.49 7.20e-01 1.93e+00 3.89e+01 angle pdb=" CA GLY N 6 " pdb=" C GLY N 6 " pdb=" O GLY N 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY M 6 " pdb=" C GLY M 6 " pdb=" O GLY M 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY I 6 " pdb=" C GLY I 6 " pdb=" O GLY I 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY O 6 " pdb=" C GLY O 6 " pdb=" O GLY O 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 ... (remaining 55479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 22972 35.60 - 71.21: 835 71.21 - 106.81: 73 106.81 - 142.41: 8 142.41 - 178.02: 4 Dihedral angle restraints: 23892 sinusoidal: 9360 harmonic: 14532 Sorted by residual: dihedral pdb=" C3 CAP H 501 " pdb=" C CAP H 501 " pdb=" C2 CAP H 501 " pdb=" O6 CAP H 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.12 -178.02 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP F 501 " pdb=" C CAP F 501 " pdb=" C2 CAP F 501 " pdb=" O6 CAP F 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.14 -177.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP B 501 " pdb=" C CAP B 501 " pdb=" C2 CAP B 501 " pdb=" O6 CAP B 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.14 -177.99 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 23889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3000 0.076 - 0.152: 2458 0.152 - 0.228: 510 0.228 - 0.305: 16 0.305 - 0.381: 8 Chirality restraints: 5992 Sorted by residual: chirality pdb=" CB HLU E 174 " pdb=" CA HLU E 174 " pdb=" CG HLU E 174 " pdb=" OH HLU E 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB HLU F 174 " pdb=" CA HLU F 174 " pdb=" CG HLU F 174 " pdb=" OH HLU F 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB HLU A 174 " pdb=" CA HLU A 174 " pdb=" CG HLU A 174 " pdb=" OH HLU A 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5989 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 298 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C ARG A 298 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG A 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 299 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 298 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ARG E 298 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG E 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA E 299 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 298 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ARG D 298 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG D 298 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA D 299 " 0.008 2.00e-02 2.50e+03 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1106 2.71 - 3.25: 39138 3.25 - 3.80: 63689 3.80 - 4.35: 89971 4.35 - 4.90: 136140 Nonbonded interactions: 330044 Sorted by model distance: nonbonded pdb=" O PRO i 75 " pdb=" CZ2 TRP l 73 " model vdw 2.157 3.340 nonbonded pdb=" O PRO k 75 " pdb=" CZ2 TRP j 73 " model vdw 2.165 3.340 nonbonded pdb=" CZ2 TRP i 73 " pdb=" O PRO j 75 " model vdw 2.233 3.340 nonbonded pdb=" CZ2 TRP k 73 " pdb=" O PRO l 75 " model vdw 2.253 3.340 nonbonded pdb=" NE ARG F 90 " pdb=" OD2 ASP F 92 " model vdw 2.255 2.520 ... (remaining 330039 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.040 Extract box with map and model: 5.770 Check model and map are aligned: 0.560 Set scattering table: 0.360 Process input model: 100.580 Find NCS groups from input model: 3.340 Set up NCS constraints: 1.510 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: 0.030 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 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 : 0.014 0.077 40876 Z= 0.893 Angle : 1.490 10.817 55484 Z= 1.111 Chirality : 0.094 0.381 5992 Planarity : 0.003 0.014 7120 Dihedral : 17.332 178.016 14644 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 7.75 % Allowed : 8.11 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.45 (0.09), residues: 4816 helix: -1.73 (0.09), residues: 1896 sheet: -0.04 (0.21), residues: 440 loop : -1.81 (0.10), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 218 HIS 0.005 0.001 HIS H 146 PHE 0.011 0.001 PHE C 367 TYR 0.017 0.002 TYR G 16 ARG 0.005 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 814 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.5436 (m) cc_final: 0.5131 (t) REVERT: A 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5189 (mtp) REVERT: A 37 ASN cc_start: 0.5643 (m-40) cc_final: 0.4764 (p0) REVERT: A 90 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3832 (tmt90) REVERT: A 207 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.4817 (t70) REVERT: B 20 VAL cc_start: 0.5436 (m) cc_final: 0.5128 (t) REVERT: B 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5166 (mtp) REVERT: B 37 ASN cc_start: 0.5633 (m-40) cc_final: 0.4761 (p0) REVERT: B 207 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4793 (t70) REVERT: C 20 VAL cc_start: 0.5437 (m) cc_final: 0.5131 (t) REVERT: C 26 MET cc_start: 0.5435 (mtt) cc_final: 0.5161 (mtp) REVERT: C 37 ASN cc_start: 0.5605 (m-40) cc_final: 0.4736 (p0) REVERT: C 207 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.4784 (t70) REVERT: D 20 VAL cc_start: 0.5404 (m) cc_final: 0.5091 (t) REVERT: D 26 MET cc_start: 0.5465 (mtt) cc_final: 0.5186 (mtp) REVERT: D 37 ASN cc_start: 0.5658 (m-40) cc_final: 0.4773 (p0) REVERT: D 207 ASP cc_start: 0.5378 (OUTLIER) cc_final: 0.4796 (t70) REVERT: E 20 VAL cc_start: 0.5409 (m) cc_final: 0.5092 (t) REVERT: E 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5162 (mtp) REVERT: E 37 ASN cc_start: 0.5628 (m-40) cc_final: 0.4769 (p0) REVERT: E 207 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4748 (t70) REVERT: F 20 VAL cc_start: 0.5405 (m) cc_final: 0.5091 (t) REVERT: F 26 MET cc_start: 0.5468 (mtt) cc_final: 0.5187 (mtp) REVERT: F 37 ASN cc_start: 0.5709 (m-40) cc_final: 0.4822 (p0) REVERT: F 207 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4821 (t70) REVERT: G 20 VAL cc_start: 0.5461 (m) cc_final: 0.5139 (t) REVERT: G 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5180 (mtp) REVERT: G 37 ASN cc_start: 0.5627 (m-40) cc_final: 0.4705 (p0) REVERT: G 207 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.4789 (t70) REVERT: H 20 VAL cc_start: 0.5434 (m) cc_final: 0.5127 (t) REVERT: H 26 MET cc_start: 0.5460 (mtt) cc_final: 0.5192 (mtp) REVERT: H 37 ASN cc_start: 0.5586 (m-40) cc_final: 0.4722 (p0) REVERT: H 207 ASP cc_start: 0.5335 (OUTLIER) cc_final: 0.4752 (t70) REVERT: i 76 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5636 (ttt180) REVERT: k 76 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5567 (ttt180) REVERT: j 76 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.5604 (ttt180) REVERT: l 76 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5522 (ttt180) outliers start: 316 outliers final: 72 residues processed: 967 average time/residue: 1.7334 time to fit residues: 1998.9281 Evaluate side-chains 638 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 553 time to evaluate : 4.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 444 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain k residue 76 ARG Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain l residue 76 ARG Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 89 MET Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 89 MET Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 89 MET Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 4.9990 chunk 369 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 448 GLN A 452 ASN B 211 ASN B 448 GLN B 452 ASN C 211 ASN C 448 GLN C 452 ASN D 211 ASN D 448 GLN D 452 ASN E 211 ASN E 452 ASN F 211 ASN F 448 GLN F 452 ASN G 211 ASN G 448 GLN G 452 ASN H 211 ASN H 452 ASN I 131 GLN J 131 GLN J 133 ASN K 131 GLN L 131 GLN L 133 ASN M 131 GLN N 131 GLN N 133 ASN O 131 GLN P 131 GLN P 133 ASN h 91 GLN g 91 GLN f 91 GLN e 91 GLN d 91 GLN c 91 GLN b 91 GLN a 91 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4584 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 40876 Z= 0.177 Angle : 0.571 5.220 55484 Z= 0.310 Chirality : 0.044 0.176 5992 Planarity : 0.004 0.034 7120 Dihedral : 10.368 179.440 5953 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.26 % Allowed : 10.59 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.18 (0.11), residues: 4816 helix: 1.11 (0.12), residues: 1848 sheet: -0.49 (0.17), residues: 800 loop : -1.02 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 218 HIS 0.006 0.001 HIS H 356 PHE 0.011 0.001 PHE I 98 TYR 0.012 0.001 TYR G 89 ARG 0.003 0.000 ARG N 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 572 time to evaluate : 4.036 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: A 20 VAL cc_start: 0.5306 (m) cc_final: 0.5061 (t) REVERT: A 26 MET cc_start: 0.5484 (mtt) cc_final: 0.5204 (mtp) REVERT: A 37 ASN cc_start: 0.5583 (m-40) cc_final: 0.4607 (p0) REVERT: A 207 ASP cc_start: 0.5557 (OUTLIER) cc_final: 0.5024 (t70) REVERT: B 20 VAL cc_start: 0.5298 (m) cc_final: 0.5056 (t) REVERT: B 26 MET cc_start: 0.5455 (mtt) cc_final: 0.5177 (mtp) REVERT: B 37 ASN cc_start: 0.5525 (m-40) cc_final: 0.4572 (p0) REVERT: B 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5000 (t70) REVERT: B 399 ASP cc_start: 0.4403 (OUTLIER) cc_final: 0.4152 (p0) REVERT: C 20 VAL cc_start: 0.5301 (m) cc_final: 0.5053 (t) REVERT: C 26 MET cc_start: 0.5454 (mtt) cc_final: 0.5155 (mtp) REVERT: C 37 ASN cc_start: 0.5550 (m-40) cc_final: 0.4580 (p0) REVERT: C 207 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.4997 (t70) REVERT: C 399 ASP cc_start: 0.4411 (OUTLIER) cc_final: 0.4160 (p0) REVERT: D 20 VAL cc_start: 0.5263 (m) cc_final: 0.5016 (t) REVERT: D 26 MET cc_start: 0.5492 (mtt) cc_final: 0.5196 (mtp) REVERT: D 37 ASN cc_start: 0.5598 (m-40) cc_final: 0.4579 (p0) REVERT: D 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5001 (t70) REVERT: E 20 VAL cc_start: 0.5270 (m) cc_final: 0.5019 (t) REVERT: E 26 MET cc_start: 0.5448 (mtt) cc_final: 0.5161 (mtp) REVERT: E 37 ASN cc_start: 0.5534 (m-40) cc_final: 0.4571 (p0) REVERT: E 207 ASP cc_start: 0.5491 (OUTLIER) cc_final: 0.4961 (t70) REVERT: E 399 ASP cc_start: 0.4383 (OUTLIER) cc_final: 0.4129 (p0) REVERT: F 20 VAL cc_start: 0.5262 (m) cc_final: 0.5016 (t) REVERT: F 26 MET cc_start: 0.5522 (mtt) cc_final: 0.5226 (mtp) REVERT: F 37 ASN cc_start: 0.5619 (m-40) cc_final: 0.4608 (p0) REVERT: F 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5000 (t70) REVERT: F 399 ASP cc_start: 0.4382 (OUTLIER) cc_final: 0.4131 (p0) REVERT: G 20 VAL cc_start: 0.5262 (m) cc_final: 0.5017 (t) REVERT: G 26 MET cc_start: 0.5513 (mtt) cc_final: 0.5203 (mtp) REVERT: G 37 ASN cc_start: 0.5574 (m-40) cc_final: 0.4530 (p0) REVERT: G 207 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4993 (t70) REVERT: G 399 ASP cc_start: 0.4390 (OUTLIER) cc_final: 0.4136 (p0) REVERT: H 20 VAL cc_start: 0.5291 (m) cc_final: 0.5053 (t) REVERT: H 26 MET cc_start: 0.5485 (mtt) cc_final: 0.5203 (mtp) REVERT: H 37 ASN cc_start: 0.5530 (m-40) cc_final: 0.4536 (p0) REVERT: H 207 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4964 (t70) REVERT: H 399 ASP cc_start: 0.4367 (OUTLIER) cc_final: 0.4118 (p0) REVERT: I 94 CYS cc_start: 0.4969 (m) cc_final: 0.4368 (t) REVERT: J 94 CYS cc_start: 0.4966 (m) cc_final: 0.4363 (t) REVERT: K 94 CYS cc_start: 0.4917 (m) cc_final: 0.4333 (t) REVERT: L 94 CYS cc_start: 0.4965 (m) cc_final: 0.4362 (t) REVERT: L 117 GLU cc_start: 0.4666 (pm20) cc_final: 0.4413 (pm20) REVERT: M 94 CYS cc_start: 0.4959 (m) cc_final: 0.4361 (t) REVERT: N 70 GLU cc_start: 0.4479 (mm-30) cc_final: 0.4222 (mm-30) REVERT: N 94 CYS cc_start: 0.4917 (m) cc_final: 0.4332 (t) REVERT: N 117 GLU cc_start: 0.4667 (pm20) cc_final: 0.4416 (pm20) REVERT: O 94 CYS cc_start: 0.4966 (m) cc_final: 0.4364 (t) REVERT: P 94 CYS cc_start: 0.4960 (m) cc_final: 0.4360 (t) REVERT: i 73 TRP cc_start: 0.7069 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: k 73 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: j 73 TRP cc_start: 0.7027 (OUTLIER) cc_final: 0.6388 (m-90) REVERT: l 73 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6527 (m-10) outliers start: 133 outliers final: 47 residues processed: 673 average time/residue: 1.8315 time to fit residues: 1459.8112 Evaluate side-chains 610 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 545 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 443 optimal weight: 7.9990 chunk 479 optimal weight: 9.9990 chunk 395 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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: