Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 08:30:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/07_2023/7yk5_33887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/07_2023/7yk5_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_33887/07_2023/7yk5_33887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/07_2023/7yk5_33887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/07_2023/7yk5_33887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/07_2023/7yk5_33887_updated.pdb" } resolution = 2.0 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= 0.001 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 17.70, per 1000 atoms: 0.44 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: 17.64 Conformation dependent library (CDL) restraints added in 5.5 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: 3.71 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: 14.53 Time building geometry restraints manager: 18.45 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: 1.000 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: 0.030 Extract box with map and model: 7.410 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 94.650 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.600 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.700 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 316 outliers final: 72 residues processed: 967 average time/residue: 1.6683 time to fit residues: 1930.6431 Evaluate side-chains 625 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 553 time to evaluate : 4.479 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 56 residues processed: 16 average time/residue: 1.5693 time to fit residues: 36.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 205 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 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: 1.9990 chunk 284 optimal weight: 7.9990 chunk 443 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 37 ASN C 211 ASN 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 37 ASN G 211 ASN G 448 GLN G 452 ASN H 37 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: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4571 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 40876 Z= 0.162 Angle : 0.551 5.089 55484 Z= 0.298 Chirality : 0.044 0.174 5992 Planarity : 0.004 0.034 7120 Dihedral : 8.322 179.994 5760 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.87 % 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: -0.11 (0.11), residues: 4816 helix: 1.19 (0.12), residues: 1848 sheet: -0.48 (0.17), residues: 800 loop : -1.00 (0.12), residues: 2168 *********************** 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 677 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 560 time to evaluate : 4.770 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 outliers start: 117 outliers final: 48 residues processed: 650 average time/residue: 1.7969 time to fit residues: 1386.6994 Evaluate side-chains 569 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 521 time to evaluate : 4.483 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 45 residues processed: 3 average time/residue: 2.7225 time to fit residues: 15.0128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 443 optimal weight: 10.0000 chunk 479 optimal weight: 9.9990 chunk 395 optimal weight: 9.9990 chunk 440 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 B 211 ASN B 448 GLN C 211 ASN C 448 GLN D 211 ASN D 448 GLN E 211 ASN E 448 GLN F 211 ASN F 448 GLN G 211 ASN G 448 GLN H 211 ASN H 448 GLN I 131 GLN K 131 GLN M 131 GLN O 131 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4645 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 40876 Z= 0.307 Angle : 0.729 5.844 55484 Z= 0.394 Chirality : 0.050 0.179 5992 Planarity : 0.005 0.033 7120 Dihedral : 9.141 179.364 5760 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.82 % 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: -0.04 (0.11), residues: 4816 helix: 1.09 (0.12), residues: 1896 sheet: -0.33 (0.17), residues: 776 loop : -0.89 (0.12), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 3 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 641 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 526 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 57 residues processed: 629 average time/residue: 1.7947 time to fit residues: 1341.3899 Evaluate side-chains 590 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 533 time to evaluate : 4.364 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 55 residues processed: 2 average time/residue: 2.7047 time to fit residues: 11.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 445 optimal weight: 1.9990 chunk 471 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN I 131 GLN K 131 GLN M 131 GLN O 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4643 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 40876 Z= 0.281 Angle : 0.698 5.709 55484 Z= 0.378 Chirality : 0.048 0.180 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.146 179.402 5760 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.11 % 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: 0.03 (0.11), residues: 4816 helix: 1.15 (0.12), residues: 1904 sheet: -0.26 (0.17), residues: 776 loop : -0.86 (0.12), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 4 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 612 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 526 time to evaluate : 4.557 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 outliers start: 86 outliers final: 60 residues processed: 608 average time/residue: 1.8870 time to fit residues: 1353.7800 Evaluate side-chains 619 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 559 time to evaluate : 4.399 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 58 residues processed: 2 average time/residue: 2.7850 time to fit residues: 12.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 402 optimal weight: 7.9990 chunk 326 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 0.0170 chunk 423 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN I 131 GLN K 131 GLN M 131 GLN O 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4637 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 40876 Z= 0.245 Angle : 0.650 5.547 55484 Z= 0.351 Chirality : 0.047 0.179 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.042 179.014 5760 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.48 % 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: 0.14 (0.11), residues: 4816 helix: 1.36 (0.12), residues: 1856 sheet: -0.27 (0.17), residues: 800 loop : -0.85 (0.12), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 5 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 640 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 539 time to evaluate : 4.484 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 outliers start: 101 outliers final: 57 residues processed: 626 average time/residue: 1.9091 time to fit residues: 1407.6474 Evaluate side-chains 599 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 542 time to evaluate : 4.500 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 51 residues processed: 6 average time/residue: 2.2667 time to fit residues: 22.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 8.9990 chunk 424 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 276 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 472 optimal weight: 1.9990 chunk 391 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN I 131 GLN K 131 GLN M 131 GLN O 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 40876 Z= 0.191 Angle : 0.577 5.286 55484 Z= 0.311 Chirality : 0.044 0.177 5992 Planarity : 0.004 0.036 7120 Dihedral : 8.729 178.679 5760 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.67 % 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: 0.32 (0.12), residues: 4816 helix: 1.57 (0.12), residues: 1840 sheet: -0.08 (0.18), residues: 792 loop : -0.83 (0.12), residues: 2184 *********************** REFINEMENT MACRO_CYCLE 6 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 611 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 543 time to evaluate : 4.439 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 outliers start: 68 outliers final: 53 residues processed: 608 average time/residue: 1.8546 time to fit residues: 1333.1317 Evaluate side-chains 585 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 532 time to evaluate : 5.089 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 51 residues processed: 2 average time/residue: 2.9377 time to fit residues: 13.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 397 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 chunk 294 optimal weight: 0.4980 chunk 286 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4652 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 40876 Z= 0.302 Angle : 0.722 5.885 55484 Z= 0.389 Chirality : 0.049 0.181 5992 Planarity : 0.005 0.033 7120 Dihedral : 9.261 179.687 5760 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.76 % 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: 0.08 (0.11), residues: 4816 helix: 1.20 (0.12), residues: 1888 sheet: -0.16 (0.17), residues: 776 loop : -0.86 (0.12), residues: 2152 *********************** REFINEMENT MACRO_CYCLE 7 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 615 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 543 time to evaluate : 4.867 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 outliers start: 72 outliers final: 53 residues processed: 613 average time/residue: 1.9027 time to fit residues: 1374.3195 Evaluate side-chains 573 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 520 time to evaluate : 4.402 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 51 residues processed: 2 average time/residue: 2.7228 time to fit residues: 11.8001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 146 HIS B 448 GLN C 146 HIS D 146 HIS E 146 HIS F 146 HIS G 146 HIS H 146 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.059 40876 Z= 0.500 Angle : 0.959 6.859 55484 Z= 0.521 Chirality : 0.058 0.221 5992 Planarity : 0.007 0.045 7120 Dihedral : 9.730 179.243 5760 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 1.64 % 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: -0.36 (0.11), residues: 4816 helix: 0.67 (0.11), residues: 1896 sheet: -0.55 (0.18), residues: 704 loop : -0.87 (0.11), residues: 2216 *********************** REFINEMENT MACRO_CYCLE 8 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 560 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 493 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 52 residues processed: 558 average time/residue: 1.8854 time to fit residues: 1241.6813 Evaluate side-chains 595 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 543 time to evaluate : 4.168 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 51 residues processed: 1 average time/residue: 2.6367 time to fit residues: 8.6252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 0.7980 chunk 450 optimal weight: 5.9990 chunk 411 optimal weight: 7.9990 chunk 438 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 396 optimal weight: 1.9990 chunk 414 optimal weight: 3.9990 chunk 436 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4639 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 40876 Z= 0.249 Angle : 0.664 5.581 55484 Z= 0.359 Chirality : 0.047 0.180 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.188 179.283 5760 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.50 % 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: 0.04 (0.11), residues: 4816 helix: 1.26 (0.12), residues: 1848 sheet: -0.37 (0.17), residues: 784 loop : -0.85 (0.12), residues: 2184 *********************** REFINEMENT MACRO_CYCLE 9 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 614 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 553 time to evaluate : 4.977 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 outliers start: 61 outliers final: 52 residues processed: 613 average time/residue: 1.9803 time to fit residues: 1426.4453 Evaluate side-chains 581 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 529 time to evaluate : 4.929 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 51 residues processed: 1 average time/residue: 2.7350 time to fit residues: 9.5712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 3.9990 chunk 463 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 chunk 486 optimal weight: 9.9990 chunk 447 optimal weight: 8.9990 chunk 387 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4644 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 40876 Z= 0.271 Angle : 0.693 5.685 55484 Z= 0.373 Chirality : 0.048 0.179 5992 Planarity : 0.005 0.035 7120 Dihedral : 9.259 179.451 5760 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.30 % 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: 0.07 (0.11), residues: 4816 helix: 1.29 (0.12), residues: 1848 sheet: -0.32 (0.17), residues: 784 loop : -0.85 (0.11), residues: 2184 ********************** REFINEMENT MACRO_CYCLE 10 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 572 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 519 time to evaluate : 4.739 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 outliers start: 53 outliers final: 52 residues processed: 571 average time/residue: 1.8432 time to fit residues: 1247.7973 Evaluate side-chains 548 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 496 time to evaluate : 4.404 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 51 residues processed: 1 average time/residue: 2.6746 time to fit residues: 8.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 20.0000 chunk 412 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 387 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 398 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.137637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.122525 restraints weight = 22754.704| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.32 r_work: 0.3059 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 1.63 restraints_weight: 0.2500 r_work: 0.2892 rms_B_bonded: 2.94 restraints_weight: 0.1250 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 40876 Z= 0.283 Angle : 0.704 5.713 55484 Z= 0.380 Chirality : 0.048 0.179 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.278 179.389 5760 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.50 % 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: 0.05 (0.11), residues: 4816 helix: 1.26 (0.12), residues: 1848 sheet: -0.33 (0.17), residues: 784 loop : -0.86 (0.11), residues: 2184 =============================================================================== Job complete usr+sys time: 18959.35 seconds wall clock time: 334 minutes 56.92 seconds (20096.92 seconds total)