Starting phenix.real_space_refine on Sun Mar 24 05:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk5_33887/03_2024/7yk5_33887_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 248 5.16 5 C 25288 2.51 5 N 6844 2.21 5 O 7552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 253": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 112": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 18.34, per 1000 atoms: 0.46 Number of scatterers: 39948 At special positions: 0 Unit cell: (136.422, 136.422, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 16 15.00 O 7552 8.00 N 6844 7.00 C 25288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.47 Conformation dependent library (CDL) restraints added in 7.1 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: 8.18 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: 12.99 Time building geometry restraints manager: 17.32 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.230 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 97.300 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.570 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.077 40876 Z= 0.893 Angle : 1.490 10.817 55484 Z= 1.111 Chirality : 0.094 0.381 5992 Planarity : 0.003 0.014 7120 Dihedral : 17.332 178.016 14644 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 7.75 % Allowed : 8.11 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.09), residues: 4816 helix: -1.73 (0.09), residues: 1896 sheet: -0.04 (0.21), residues: 440 loop : -1.81 (0.10), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 218 HIS 0.005 0.001 HIS H 146 PHE 0.011 0.001 PHE C 367 TYR 0.017 0.002 TYR G 16 ARG 0.005 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 814 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.5436 (m) cc_final: 0.5131 (t) REVERT: A 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5189 (mtp) REVERT: A 37 ASN cc_start: 0.5643 (m-40) cc_final: 0.4764 (p0) REVERT: A 90 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3832 (tmt90) REVERT: A 207 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.4817 (t70) REVERT: B 20 VAL cc_start: 0.5436 (m) cc_final: 0.5128 (t) REVERT: B 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5166 (mtp) REVERT: B 37 ASN cc_start: 0.5633 (m-40) cc_final: 0.4761 (p0) REVERT: B 207 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4793 (t70) REVERT: C 20 VAL cc_start: 0.5437 (m) cc_final: 0.5131 (t) REVERT: C 26 MET cc_start: 0.5435 (mtt) cc_final: 0.5161 (mtp) REVERT: C 37 ASN cc_start: 0.5605 (m-40) cc_final: 0.4736 (p0) REVERT: C 207 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.4784 (t70) REVERT: D 20 VAL cc_start: 0.5404 (m) cc_final: 0.5091 (t) REVERT: D 26 MET cc_start: 0.5465 (mtt) cc_final: 0.5186 (mtp) REVERT: D 37 ASN cc_start: 0.5658 (m-40) cc_final: 0.4773 (p0) REVERT: D 207 ASP cc_start: 0.5378 (OUTLIER) cc_final: 0.4796 (t70) REVERT: E 20 VAL cc_start: 0.5409 (m) cc_final: 0.5092 (t) REVERT: E 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5162 (mtp) REVERT: E 37 ASN cc_start: 0.5628 (m-40) cc_final: 0.4769 (p0) REVERT: E 207 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4748 (t70) REVERT: F 20 VAL cc_start: 0.5405 (m) cc_final: 0.5091 (t) REVERT: F 26 MET cc_start: 0.5468 (mtt) cc_final: 0.5187 (mtp) REVERT: F 37 ASN cc_start: 0.5709 (m-40) cc_final: 0.4822 (p0) REVERT: F 207 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4821 (t70) REVERT: G 20 VAL cc_start: 0.5461 (m) cc_final: 0.5139 (t) REVERT: G 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5180 (mtp) REVERT: G 37 ASN cc_start: 0.5627 (m-40) cc_final: 0.4705 (p0) REVERT: G 207 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.4789 (t70) REVERT: H 20 VAL cc_start: 0.5434 (m) cc_final: 0.5127 (t) REVERT: H 26 MET cc_start: 0.5460 (mtt) cc_final: 0.5192 (mtp) REVERT: H 37 ASN cc_start: 0.5586 (m-40) cc_final: 0.4722 (p0) REVERT: H 207 ASP cc_start: 0.5335 (OUTLIER) cc_final: 0.4752 (t70) REVERT: i 76 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5636 (ttt180) REVERT: k 76 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5567 (ttt180) REVERT: j 76 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.5604 (ttt180) REVERT: l 76 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5522 (ttt180) outliers start: 316 outliers final: 72 residues processed: 967 average time/residue: 1.6437 time to fit residues: 1898.5670 Evaluate side-chains 638 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 553 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 444 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain k residue 76 ARG Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain l residue 76 ARG Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 89 MET Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 89 MET Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 89 MET Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 4.9990 chunk 369 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 448 GLN A 452 ASN B 211 ASN B 448 GLN B 452 ASN C 211 ASN C 448 GLN C 452 ASN D 211 ASN D 448 GLN D 452 ASN E 211 ASN E 452 ASN F 211 ASN F 448 GLN F 452 ASN G 211 ASN G 448 GLN G 452 ASN H 211 ASN H 452 ASN I 131 GLN J 131 GLN J 133 ASN K 131 GLN L 131 GLN L 133 ASN M 131 GLN N 131 GLN N 133 ASN O 131 GLN P 131 GLN P 133 ASN h 91 GLN g 91 GLN f 91 GLN e 91 GLN d 91 GLN c 91 GLN b 91 GLN a 91 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4584 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 40876 Z= 0.177 Angle : 0.571 5.220 55484 Z= 0.310 Chirality : 0.044 0.176 5992 Planarity : 0.004 0.034 7120 Dihedral : 10.368 179.440 5953 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.26 % Allowed : 10.59 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 4816 helix: 1.11 (0.12), residues: 1848 sheet: -0.49 (0.17), residues: 800 loop : -1.02 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 218 HIS 0.006 0.001 HIS H 356 PHE 0.011 0.001 PHE I 98 TYR 0.012 0.001 TYR G 89 ARG 0.003 0.000 ARG N 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 572 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.5306 (m) cc_final: 0.5061 (t) REVERT: A 26 MET cc_start: 0.5484 (mtt) cc_final: 0.5204 (mtp) REVERT: A 37 ASN cc_start: 0.5583 (m-40) cc_final: 0.4607 (p0) REVERT: A 207 ASP cc_start: 0.5557 (OUTLIER) cc_final: 0.5024 (t70) REVERT: B 20 VAL cc_start: 0.5298 (m) cc_final: 0.5056 (t) REVERT: B 26 MET cc_start: 0.5455 (mtt) cc_final: 0.5177 (mtp) REVERT: B 37 ASN cc_start: 0.5525 (m-40) cc_final: 0.4572 (p0) REVERT: B 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5000 (t70) REVERT: B 399 ASP cc_start: 0.4403 (OUTLIER) cc_final: 0.4152 (p0) REVERT: C 20 VAL cc_start: 0.5301 (m) cc_final: 0.5053 (t) REVERT: C 26 MET cc_start: 0.5454 (mtt) cc_final: 0.5155 (mtp) REVERT: C 37 ASN cc_start: 0.5550 (m-40) cc_final: 0.4580 (p0) REVERT: C 207 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.4997 (t70) REVERT: C 399 ASP cc_start: 0.4411 (OUTLIER) cc_final: 0.4160 (p0) REVERT: D 20 VAL cc_start: 0.5263 (m) cc_final: 0.5016 (t) REVERT: D 26 MET cc_start: 0.5492 (mtt) cc_final: 0.5196 (mtp) REVERT: D 37 ASN cc_start: 0.5598 (m-40) cc_final: 0.4579 (p0) REVERT: D 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5001 (t70) REVERT: E 20 VAL cc_start: 0.5270 (m) cc_final: 0.5019 (t) REVERT: E 26 MET cc_start: 0.5448 (mtt) cc_final: 0.5161 (mtp) REVERT: E 37 ASN cc_start: 0.5534 (m-40) cc_final: 0.4571 (p0) REVERT: E 207 ASP cc_start: 0.5491 (OUTLIER) cc_final: 0.4961 (t70) REVERT: E 399 ASP cc_start: 0.4383 (OUTLIER) cc_final: 0.4129 (p0) REVERT: F 20 VAL cc_start: 0.5262 (m) cc_final: 0.5016 (t) REVERT: F 26 MET cc_start: 0.5522 (mtt) cc_final: 0.5226 (mtp) REVERT: F 37 ASN cc_start: 0.5619 (m-40) cc_final: 0.4608 (p0) REVERT: F 207 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5000 (t70) REVERT: F 399 ASP cc_start: 0.4382 (OUTLIER) cc_final: 0.4131 (p0) REVERT: G 20 VAL cc_start: 0.5262 (m) cc_final: 0.5017 (t) REVERT: G 26 MET cc_start: 0.5513 (mtt) cc_final: 0.5203 (mtp) REVERT: G 37 ASN cc_start: 0.5574 (m-40) cc_final: 0.4530 (p0) REVERT: G 207 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4993 (t70) REVERT: G 399 ASP cc_start: 0.4390 (OUTLIER) cc_final: 0.4136 (p0) REVERT: H 20 VAL cc_start: 0.5291 (m) cc_final: 0.5053 (t) REVERT: H 26 MET cc_start: 0.5485 (mtt) cc_final: 0.5203 (mtp) REVERT: H 37 ASN cc_start: 0.5530 (m-40) cc_final: 0.4536 (p0) REVERT: H 207 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4964 (t70) REVERT: H 399 ASP cc_start: 0.4367 (OUTLIER) cc_final: 0.4118 (p0) REVERT: I 94 CYS cc_start: 0.4969 (m) cc_final: 0.4368 (t) REVERT: J 94 CYS cc_start: 0.4966 (m) cc_final: 0.4363 (t) REVERT: K 94 CYS cc_start: 0.4917 (m) cc_final: 0.4333 (t) REVERT: L 94 CYS cc_start: 0.4965 (m) cc_final: 0.4362 (t) REVERT: L 117 GLU cc_start: 0.4666 (pm20) cc_final: 0.4413 (pm20) REVERT: M 94 CYS cc_start: 0.4959 (m) cc_final: 0.4361 (t) REVERT: N 70 GLU cc_start: 0.4479 (mm-30) cc_final: 0.4222 (mm-30) REVERT: N 94 CYS cc_start: 0.4917 (m) cc_final: 0.4332 (t) REVERT: N 117 GLU cc_start: 0.4667 (pm20) cc_final: 0.4416 (pm20) REVERT: O 94 CYS cc_start: 0.4966 (m) cc_final: 0.4364 (t) REVERT: P 94 CYS cc_start: 0.4960 (m) cc_final: 0.4360 (t) REVERT: i 73 TRP cc_start: 0.7069 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: k 73 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: j 73 TRP cc_start: 0.7027 (OUTLIER) cc_final: 0.6388 (m-90) REVERT: l 73 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6527 (m-10) outliers start: 133 outliers final: 47 residues processed: 673 average time/residue: 1.6942 time to fit residues: 1351.6892 Evaluate side-chains 610 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 545 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 443 optimal weight: 7.9990 chunk 479 optimal weight: 9.9990 chunk 395 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 J 131 GLN K 131 GLN L 131 GLN M 131 GLN N 131 GLN O 131 GLN P 131 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4647 moved from start: 0.1965 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= 0.301 Angle : 0.724 5.842 55484 Z= 0.392 Chirality : 0.049 0.180 5992 Planarity : 0.005 0.034 7120 Dihedral : 10.399 179.385 5878 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.57 % Allowed : 10.32 % Favored : 87.11 % 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: -0.06 (0.11), residues: 4816 helix: 1.07 (0.12), residues: 1896 sheet: -0.31 (0.17), residues: 776 loop : -0.91 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 218 HIS 0.005 0.002 HIS D 356 PHE 0.016 0.002 PHE E 44 TYR 0.015 0.002 TYR G 89 ARG 0.006 0.001 ARG D 315 *********************** 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 639 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 534 time to evaluate : 4.581 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: A 26 MET cc_start: 0.5669 (mtt) cc_final: 0.5403 (mtp) REVERT: A 90 ARG cc_start: 0.4810 (OUTLIER) cc_final: 0.3740 (tmt90) REVERT: A 189 TYR cc_start: 0.5033 (OUTLIER) cc_final: 0.4829 (t80) REVERT: A 207 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.4968 (t70) REVERT: B 26 MET cc_start: 0.5642 (mtt) cc_final: 0.5379 (mtp) REVERT: B 189 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.4843 (t80) REVERT: B 207 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.4943 (t70) REVERT: C 26 MET cc_start: 0.5640 (mtt) cc_final: 0.5370 (mtp) REVERT: C 189 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.4863 (t80) REVERT: C 207 ASP cc_start: 0.5450 (OUTLIER) cc_final: 0.4941 (t70) REVERT: C 308 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4557 (ttpp) REVERT: D 26 MET cc_start: 0.5668 (mtt) cc_final: 0.5392 (mtp) REVERT: D 189 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4844 (t80) REVERT: D 207 ASP cc_start: 0.5454 (OUTLIER) cc_final: 0.4941 (t70) REVERT: E 26 MET cc_start: 0.5642 (mtt) cc_final: 0.5380 (mtp) REVERT: E 189 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4900 (t80) REVERT: E 207 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.4905 (t70) REVERT: F 26 MET cc_start: 0.5669 (mtt) cc_final: 0.5392 (mtp) REVERT: F 189 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.4881 (t80) REVERT: F 207 ASP cc_start: 0.5457 (OUTLIER) cc_final: 0.4942 (t70) REVERT: G 26 MET cc_start: 0.5662 (mtt) cc_final: 0.5387 (mtp) REVERT: G 189 TYR cc_start: 0.5081 (OUTLIER) cc_final: 0.4875 (t80) REVERT: G 207 ASP cc_start: 0.5447 (OUTLIER) cc_final: 0.4938 (t70) REVERT: G 308 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4573 (ttpp) REVERT: H 26 MET cc_start: 0.5669 (mtt) cc_final: 0.5401 (mtp) REVERT: H 189 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4882 (t80) REVERT: H 207 ASP cc_start: 0.5425 (OUTLIER) cc_final: 0.4909 (t70) REVERT: H 308 LYS cc_start: 0.5277 (OUTLIER) cc_final: 0.4560 (ttpp) REVERT: I 70 GLU cc_start: 0.4745 (OUTLIER) cc_final: 0.3749 (mp0) REVERT: K 70 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.3731 (mp0) REVERT: L 70 GLU cc_start: 0.4732 (OUTLIER) cc_final: 0.3746 (mp0) REVERT: M 70 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.3758 (mp0) REVERT: N 70 GLU cc_start: 0.4470 (mm-30) cc_final: 0.4257 (mm-30) REVERT: O 70 GLU cc_start: 0.4773 (OUTLIER) cc_final: 0.3779 (mp0) REVERT: P 70 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.3753 (mp0) REVERT: i 73 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.6336 (m-90) REVERT: k 73 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6358 (m-90) REVERT: j 73 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.6438 (m-90) REVERT: l 73 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.6463 (m-90) REVERT: a 91 GLN cc_start: 0.4544 (OUTLIER) cc_final: 0.4133 (pp30) outliers start: 105 outliers final: 50 residues processed: 622 average time/residue: 1.7876 time to fit residues: 1320.5473 Evaluate side-chains 596 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 515 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 308 LYS Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 88 SER Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 7.9990 chunk 211 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 445 optimal weight: 1.9990 chunk 471 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 422 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 131 GLN J 131 GLN K 131 GLN L 131 GLN M 131 GLN N 131 GLN O 131 GLN P 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40876 Z= 0.221 Angle : 0.621 5.484 55484 Z= 0.335 Chirality : 0.046 0.178 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.988 179.008 5872 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.03 % Allowed : 10.88 % Favored : 87.08 % 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: 0.21 (0.12), residues: 4816 helix: 1.47 (0.12), residues: 1856 sheet: -0.21 (0.17), residues: 792 loop : -0.87 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 218 HIS 0.004 0.001 HIS D 146 PHE 0.020 0.002 PHE H 203 TYR 0.012 0.002 TYR H 89 ARG 0.004 0.000 ARG B 451 *********************** 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 609 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 526 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5538 (mtt) cc_final: 0.5257 (mtp) REVERT: A 90 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.3615 (tmt90) REVERT: A 207 ASP cc_start: 0.5521 (OUTLIER) cc_final: 0.4996 (t70) REVERT: B 26 MET cc_start: 0.5514 (mtt) cc_final: 0.5237 (mtp) REVERT: B 90 ARG cc_start: 0.4846 (OUTLIER) cc_final: 0.4568 (ttm170) REVERT: B 207 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.5032 (t70) REVERT: C 26 MET cc_start: 0.5510 (mtt) cc_final: 0.5226 (mtp) REVERT: C 207 ASP cc_start: 0.5537 (OUTLIER) cc_final: 0.5027 (t70) REVERT: C 308 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4513 (ttpp) REVERT: D 26 MET cc_start: 0.5541 (mtt) cc_final: 0.5250 (mtp) REVERT: D 207 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5032 (t70) REVERT: E 26 MET cc_start: 0.5512 (mtt) cc_final: 0.5234 (mtp) REVERT: E 207 ASP cc_start: 0.5503 (OUTLIER) cc_final: 0.4993 (t70) REVERT: F 26 MET cc_start: 0.5541 (mtt) cc_final: 0.5250 (mtp) REVERT: F 207 ASP cc_start: 0.5547 (OUTLIER) cc_final: 0.5031 (t70) REVERT: G 26 MET cc_start: 0.5531 (mtt) cc_final: 0.5243 (mtp) REVERT: G 207 ASP cc_start: 0.5534 (OUTLIER) cc_final: 0.5026 (t70) REVERT: H 26 MET cc_start: 0.5541 (mtt) cc_final: 0.5260 (mtp) REVERT: H 207 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.4999 (t70) REVERT: H 308 LYS cc_start: 0.5237 (OUTLIER) cc_final: 0.4525 (ttpp) REVERT: I 66 PHE cc_start: 0.4241 (t80) cc_final: 0.3820 (t80) REVERT: I 70 GLU cc_start: 0.4572 (OUTLIER) cc_final: 0.3647 (mp0) REVERT: I 94 CYS cc_start: 0.5010 (m) cc_final: 0.4367 (t) REVERT: I 117 GLU cc_start: 0.4867 (pm20) cc_final: 0.4596 (pm20) REVERT: J 66 PHE cc_start: 0.4266 (t80) cc_final: 0.3844 (t80) REVERT: J 70 GLU cc_start: 0.4574 (OUTLIER) cc_final: 0.3655 (mp0) REVERT: J 94 CYS cc_start: 0.5009 (m) cc_final: 0.4364 (t) REVERT: J 117 GLU cc_start: 0.4844 (pm20) cc_final: 0.4575 (pm20) REVERT: K 66 PHE cc_start: 0.4234 (t80) cc_final: 0.3797 (t80) REVERT: K 70 GLU cc_start: 0.4578 (OUTLIER) cc_final: 0.3655 (mp0) REVERT: K 94 CYS cc_start: 0.4966 (m) cc_final: 0.4339 (t) REVERT: L 66 PHE cc_start: 0.4230 (t80) cc_final: 0.3794 (t80) REVERT: L 70 GLU cc_start: 0.4565 (OUTLIER) cc_final: 0.3636 (mp0) REVERT: L 94 CYS cc_start: 0.5007 (m) cc_final: 0.4363 (t) REVERT: L 117 GLU cc_start: 0.4848 (pm20) cc_final: 0.4580 (pm20) REVERT: M 66 PHE cc_start: 0.4206 (t80) cc_final: 0.3776 (t80) REVERT: M 70 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.3655 (mp0) REVERT: M 94 CYS cc_start: 0.5003 (m) cc_final: 0.4362 (t) REVERT: N 94 CYS cc_start: 0.4962 (m) cc_final: 0.4335 (t) REVERT: N 117 GLU cc_start: 0.4848 (pm20) cc_final: 0.4581 (pm20) REVERT: O 66 PHE cc_start: 0.4229 (t80) cc_final: 0.3801 (t80) REVERT: O 70 GLU cc_start: 0.4570 (OUTLIER) cc_final: 0.3647 (mp0) REVERT: O 94 CYS cc_start: 0.5008 (m) cc_final: 0.4365 (t) REVERT: P 70 GLU cc_start: 0.4577 (OUTLIER) cc_final: 0.3653 (mp0) REVERT: P 94 CYS cc_start: 0.4995 (m) cc_final: 0.4355 (t) REVERT: P 117 GLU cc_start: 0.4857 (pm20) cc_final: 0.4589 (pm20) REVERT: i 73 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.6376 (m-90) REVERT: k 73 TRP cc_start: 0.7104 (OUTLIER) cc_final: 0.6382 (m-90) REVERT: j 73 TRP cc_start: 0.7102 (OUTLIER) cc_final: 0.6429 (m-90) REVERT: l 73 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6439 (m-90) REVERT: a 91 GLN cc_start: 0.4972 (OUTLIER) cc_final: 0.4452 (pp30) outliers start: 83 outliers final: 37 residues processed: 602 average time/residue: 1.8657 time to fit residues: 1318.6170 Evaluate side-chains 593 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 532 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 351 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 326 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 0.0010 chunk 423 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 211 ASN C 211 ASN D 211 ASN E 211 ASN F 211 ASN G 211 ASN H 211 ASN I 131 GLN J 131 GLN K 131 GLN L 131 GLN M 131 GLN N 131 GLN O 131 GLN P 131 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4560 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 40876 Z= 0.112 Angle : 0.458 4.849 55484 Z= 0.244 Chirality : 0.041 0.176 5992 Planarity : 0.004 0.037 7120 Dihedral : 8.917 179.244 5865 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 11.86 % Favored : 87.11 % 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: 0.70 (0.12), residues: 4816 helix: 2.07 (0.13), residues: 1784 sheet: 0.16 (0.18), residues: 792 loop : -0.76 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.002 0.001 HIS D 146 PHE 0.009 0.001 PHE B 215 TYR 0.009 0.001 TYR P 110 ARG 0.004 0.000 ARG B 451 *********************** 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 625 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 583 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5434 (mtt) cc_final: 0.5083 (mtp) REVERT: A 207 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5072 (t70) REVERT: A 448 GLN cc_start: 0.4534 (tp40) cc_final: 0.4323 (tp-100) REVERT: B 26 MET cc_start: 0.5374 (mtt) cc_final: 0.5033 (mtp) REVERT: B 207 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5168 (t70) REVERT: B 448 GLN cc_start: 0.4524 (tp40) cc_final: 0.4287 (tp-100) REVERT: C 26 MET cc_start: 0.5404 (mtt) cc_final: 0.5049 (mtp) REVERT: C 207 ASP cc_start: 0.5613 (OUTLIER) cc_final: 0.5127 (t70) REVERT: C 448 GLN cc_start: 0.4544 (tp40) cc_final: 0.4332 (tp-100) REVERT: D 26 MET cc_start: 0.5438 (mtt) cc_final: 0.5080 (mtp) REVERT: D 207 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5167 (t70) REVERT: D 448 GLN cc_start: 0.4499 (tp40) cc_final: 0.4286 (tp-100) REVERT: E 26 MET cc_start: 0.5369 (mtt) cc_final: 0.5028 (mtp) REVERT: E 207 ASP cc_start: 0.5605 (OUTLIER) cc_final: 0.5113 (t70) REVERT: E 448 GLN cc_start: 0.4520 (tp40) cc_final: 0.4310 (tp-100) REVERT: F 26 MET cc_start: 0.5438 (mtt) cc_final: 0.5078 (mtp) REVERT: F 207 ASP cc_start: 0.5635 (OUTLIER) cc_final: 0.5169 (t70) REVERT: F 448 GLN cc_start: 0.4509 (tp40) cc_final: 0.4295 (tp-100) REVERT: G 26 MET cc_start: 0.5430 (mtt) cc_final: 0.5070 (mtp) REVERT: G 207 ASP cc_start: 0.5612 (OUTLIER) cc_final: 0.5126 (t70) REVERT: G 448 GLN cc_start: 0.4480 (tp40) cc_final: 0.4252 (tp-100) REVERT: H 26 MET cc_start: 0.5401 (mtt) cc_final: 0.5057 (mtp) REVERT: H 207 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5136 (t70) REVERT: H 448 GLN cc_start: 0.4587 (tp40) cc_final: 0.4373 (tp-100) REVERT: I 94 CYS cc_start: 0.4818 (m) cc_final: 0.4267 (t) REVERT: J 93 SER cc_start: 0.4962 (t) cc_final: 0.4326 (p) REVERT: J 94 CYS cc_start: 0.4820 (m) cc_final: 0.4323 (t) REVERT: K 94 CYS cc_start: 0.4825 (m) cc_final: 0.4267 (t) REVERT: L 94 CYS cc_start: 0.4820 (m) cc_final: 0.4266 (t) REVERT: M 93 SER cc_start: 0.4890 (t) cc_final: 0.4277 (p) REVERT: M 94 CYS cc_start: 0.4819 (m) cc_final: 0.4322 (t) REVERT: N 94 CYS cc_start: 0.4816 (m) cc_final: 0.4265 (t) REVERT: O 93 SER cc_start: 0.4952 (t) cc_final: 0.4328 (p) REVERT: O 94 CYS cc_start: 0.4811 (m) cc_final: 0.4319 (t) REVERT: P 94 CYS cc_start: 0.4813 (m) cc_final: 0.4264 (t) REVERT: i 73 TRP cc_start: 0.7156 (OUTLIER) cc_final: 0.6355 (m-90) REVERT: k 73 TRP cc_start: 0.7152 (OUTLIER) cc_final: 0.6359 (m-90) REVERT: j 73 TRP cc_start: 0.7127 (OUTLIER) cc_final: 0.6461 (m-90) REVERT: l 73 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6453 (m-90) outliers start: 42 outliers final: 16 residues processed: 613 average time/residue: 1.8426 time to fit residues: 1330.8257 Evaluate side-chains 556 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 528 time to evaluate : 5.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain d residue 91 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 7.9990 chunk 424 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 276 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 472 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 211 ASN B 146 HIS B 211 ASN C 146 HIS C 211 ASN D 146 HIS D 211 ASN E 146 HIS E 211 ASN F 146 HIS F 211 ASN G 146 HIS G 211 ASN H 146 HIS H 211 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4678 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 40876 Z= 0.475 Angle : 0.919 6.528 55484 Z= 0.500 Chirality : 0.057 0.228 5992 Planarity : 0.007 0.044 7120 Dihedral : 10.393 179.470 5822 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.67 % Allowed : 10.76 % Favored : 87.57 % 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: -0.02 (0.11), residues: 4816 helix: 1.27 (0.12), residues: 1792 sheet: -0.44 (0.18), residues: 720 loop : -0.88 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP h 86 HIS 0.008 0.002 HIS F 146 PHE 0.035 0.004 PHE F 203 TYR 0.018 0.004 TYR F 304 ARG 0.015 0.001 ARG G 90 *********************** 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 579 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 511 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5700 (mtt) cc_final: 0.5446 (mtp) REVERT: A 90 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.3667 (tmt90) REVERT: A 99 ASP cc_start: 0.4122 (t0) cc_final: 0.3772 (t0) REVERT: A 189 TYR cc_start: 0.5087 (OUTLIER) cc_final: 0.4811 (t80) REVERT: A 207 ASP cc_start: 0.5513 (OUTLIER) cc_final: 0.5047 (t0) REVERT: B 26 MET cc_start: 0.5672 (mtt) cc_final: 0.5426 (mtp) REVERT: B 99 ASP cc_start: 0.4127 (t0) cc_final: 0.3779 (t0) REVERT: B 189 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4886 (t80) REVERT: B 207 ASP cc_start: 0.5481 (OUTLIER) cc_final: 0.5016 (t0) REVERT: C 26 MET cc_start: 0.5670 (mtt) cc_final: 0.5411 (mtp) REVERT: C 99 ASP cc_start: 0.4122 (t0) cc_final: 0.3773 (t0) REVERT: C 189 TYR cc_start: 0.5066 (OUTLIER) cc_final: 0.4790 (t80) REVERT: C 207 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.5018 (t0) REVERT: C 308 LYS cc_start: 0.5390 (OUTLIER) cc_final: 0.4650 (ttpp) REVERT: D 26 MET cc_start: 0.5694 (mtt) cc_final: 0.5432 (mtp) REVERT: D 99 ASP cc_start: 0.4148 (t0) cc_final: 0.3803 (t0) REVERT: D 189 TYR cc_start: 0.5066 (OUTLIER) cc_final: 0.4789 (t80) REVERT: D 207 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.5015 (t0) REVERT: E 26 MET cc_start: 0.5672 (mtt) cc_final: 0.5424 (mtp) REVERT: E 99 ASP cc_start: 0.4144 (t0) cc_final: 0.3799 (t0) REVERT: E 189 TYR cc_start: 0.5122 (OUTLIER) cc_final: 0.4886 (t80) REVERT: E 207 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.5002 (t0) REVERT: F 26 MET cc_start: 0.5697 (mtt) cc_final: 0.5434 (mtp) REVERT: F 99 ASP cc_start: 0.4139 (t0) cc_final: 0.3792 (t0) REVERT: F 189 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4809 (t80) REVERT: F 207 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.5013 (t0) REVERT: G 26 MET cc_start: 0.5688 (mtt) cc_final: 0.5426 (mtp) REVERT: G 99 ASP cc_start: 0.4145 (t0) cc_final: 0.3800 (t0) REVERT: G 189 TYR cc_start: 0.5122 (OUTLIER) cc_final: 0.4888 (t80) REVERT: G 207 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.5014 (t0) REVERT: H 26 MET cc_start: 0.5699 (mtt) cc_final: 0.5447 (mtp) REVERT: H 99 ASP cc_start: 0.4145 (t0) cc_final: 0.3801 (t0) REVERT: H 189 TYR cc_start: 0.5083 (OUTLIER) cc_final: 0.4811 (t80) REVERT: H 207 ASP cc_start: 0.5451 (OUTLIER) cc_final: 0.4979 (t0) REVERT: H 308 LYS cc_start: 0.5414 (OUTLIER) cc_final: 0.4667 (ttpp) REVERT: I 70 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.3724 (mp0) REVERT: J 70 GLU cc_start: 0.4747 (OUTLIER) cc_final: 0.3689 (mp0) REVERT: K 70 GLU cc_start: 0.4752 (OUTLIER) cc_final: 0.3735 (mp0) REVERT: L 70 GLU cc_start: 0.4737 (OUTLIER) cc_final: 0.3720 (mp0) REVERT: M 70 GLU cc_start: 0.4755 (OUTLIER) cc_final: 0.3727 (mp0) REVERT: O 70 GLU cc_start: 0.4742 (OUTLIER) cc_final: 0.3721 (mp0) REVERT: P 70 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.3725 (mp0) REVERT: i 73 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6378 (m-90) REVERT: k 73 TRP cc_start: 0.7178 (OUTLIER) cc_final: 0.6390 (m-90) REVERT: j 73 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6436 (m-90) REVERT: l 73 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.6438 (m-90) outliers start: 68 outliers final: 32 residues processed: 569 average time/residue: 1.8113 time to fit residues: 1211.8771 Evaluate side-chains 572 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 510 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain a residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 344 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 397 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 470 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 286 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4610 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 40876 Z= 0.163 Angle : 0.545 5.036 55484 Z= 0.294 Chirality : 0.043 0.178 5992 Planarity : 0.004 0.035 7120 Dihedral : 9.426 178.984 5816 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.05 % Allowed : 11.20 % Favored : 87.75 % 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: 0.42 (0.12), residues: 4816 helix: 1.79 (0.13), residues: 1784 sheet: -0.13 (0.18), residues: 800 loop : -0.81 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 86 HIS 0.003 0.001 HIS A 146 PHE 0.014 0.001 PHE F 203 TYR 0.011 0.001 TYR G 89 ARG 0.002 0.000 ARG J 69 *********************** 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 565 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 522 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5467 (mtt) cc_final: 0.5161 (mtp) REVERT: A 123 SER cc_start: 0.5042 (OUTLIER) cc_final: 0.4795 (t) REVERT: A 189 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4686 (t80) REVERT: A 207 ASP cc_start: 0.5629 (OUTLIER) cc_final: 0.5092 (t70) REVERT: B 26 MET cc_start: 0.5445 (mtt) cc_final: 0.5141 (mtp) REVERT: B 189 TYR cc_start: 0.4860 (OUTLIER) cc_final: 0.4657 (t80) REVERT: B 207 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5122 (t70) REVERT: C 26 MET cc_start: 0.5439 (mtt) cc_final: 0.5126 (mtp) REVERT: C 123 SER cc_start: 0.4977 (OUTLIER) cc_final: 0.4721 (t) REVERT: C 189 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.4680 (t80) REVERT: C 207 ASP cc_start: 0.5647 (OUTLIER) cc_final: 0.5136 (t70) REVERT: D 26 MET cc_start: 0.5450 (mtt) cc_final: 0.5131 (mtp) REVERT: D 189 TYR cc_start: 0.4884 (OUTLIER) cc_final: 0.4677 (t80) REVERT: D 207 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5122 (t70) REVERT: E 26 MET cc_start: 0.5444 (mtt) cc_final: 0.5139 (mtp) REVERT: E 123 SER cc_start: 0.5001 (OUTLIER) cc_final: 0.4743 (t) REVERT: E 189 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.4657 (t80) REVERT: E 207 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5128 (t70) REVERT: F 26 MET cc_start: 0.5451 (mtt) cc_final: 0.5132 (mtp) REVERT: F 189 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.4678 (t80) REVERT: F 207 ASP cc_start: 0.5657 (OUTLIER) cc_final: 0.5138 (t70) REVERT: G 26 MET cc_start: 0.5441 (mtt) cc_final: 0.5124 (mtp) REVERT: G 123 SER cc_start: 0.5044 (OUTLIER) cc_final: 0.4797 (t) REVERT: G 189 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.4656 (t80) REVERT: G 207 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.5122 (t70) REVERT: H 26 MET cc_start: 0.5470 (mtt) cc_final: 0.5163 (mtp) REVERT: H 123 SER cc_start: 0.4996 (OUTLIER) cc_final: 0.4738 (t) REVERT: H 189 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.4678 (t80) REVERT: H 207 ASP cc_start: 0.5623 (OUTLIER) cc_final: 0.5105 (t70) REVERT: I 94 CYS cc_start: 0.4896 (m) cc_final: 0.4311 (t) REVERT: J 27 ILE cc_start: 0.4654 (mt) cc_final: 0.4331 (mm) REVERT: J 94 CYS cc_start: 0.4894 (m) cc_final: 0.4307 (t) REVERT: K 27 ILE cc_start: 0.4654 (mt) cc_final: 0.4331 (mm) REVERT: K 94 CYS cc_start: 0.4850 (m) cc_final: 0.4285 (t) REVERT: L 27 ILE cc_start: 0.4648 (mt) cc_final: 0.4327 (mm) REVERT: L 94 CYS cc_start: 0.4893 (m) cc_final: 0.4306 (t) REVERT: M 94 CYS cc_start: 0.4890 (m) cc_final: 0.4304 (t) REVERT: N 27 ILE cc_start: 0.4608 (mt) cc_final: 0.4319 (mm) REVERT: N 94 CYS cc_start: 0.4847 (m) cc_final: 0.4276 (t) REVERT: O 27 ILE cc_start: 0.4625 (mt) cc_final: 0.4287 (mm) REVERT: O 94 CYS cc_start: 0.4889 (m) cc_final: 0.4305 (t) REVERT: P 94 CYS cc_start: 0.4886 (m) cc_final: 0.4304 (t) REVERT: i 73 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.6319 (m-90) REVERT: k 73 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6413 (m-90) REVERT: j 73 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6450 (m-90) REVERT: l 73 TRP cc_start: 0.7152 (OUTLIER) cc_final: 0.6471 (m-90) outliers start: 43 outliers final: 15 residues processed: 557 average time/residue: 1.8237 time to fit residues: 1208.8536 Evaluate side-chains 563 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 523 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain a residue 89 MET 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: 9.9990 chunk 141 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 448 GLN h 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4685 moved from start: 0.2113 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= 0.530 Angle : 0.986 7.181 55484 Z= 0.536 Chirality : 0.059 0.249 5992 Planarity : 0.007 0.054 7120 Dihedral : 10.529 179.528 5816 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.57 % Allowed : 10.34 % Favored : 88.09 % 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: -0.24 (0.11), residues: 4816 helix: 0.90 (0.12), residues: 1848 sheet: -0.54 (0.18), residues: 704 loop : -0.87 (0.11), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 218 HIS 0.006 0.002 HIS G 295 PHE 0.027 0.004 PHE F 203 TYR 0.021 0.004 TYR D 304 ARG 0.014 0.002 ARG G 315 *********************** 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 561 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 497 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5722 (mtt) cc_final: 0.5472 (mtp) REVERT: A 99 ASP cc_start: 0.4125 (t0) cc_final: 0.3785 (t0) REVERT: A 189 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.4798 (t80) REVERT: A 207 ASP cc_start: 0.5473 (OUTLIER) cc_final: 0.5012 (t0) REVERT: B 26 MET cc_start: 0.5696 (mtt) cc_final: 0.5450 (mtp) REVERT: B 99 ASP cc_start: 0.4127 (t0) cc_final: 0.3788 (t0) REVERT: B 189 TYR cc_start: 0.5107 (OUTLIER) cc_final: 0.4861 (t80) REVERT: B 207 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.4978 (t0) REVERT: C 26 MET cc_start: 0.5691 (mtt) cc_final: 0.5436 (mtp) REVERT: C 99 ASP cc_start: 0.4115 (t0) cc_final: 0.3775 (t0) REVERT: C 207 ASP cc_start: 0.5444 (OUTLIER) cc_final: 0.4989 (t0) REVERT: C 308 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4644 (ttpp) REVERT: D 26 MET cc_start: 0.5716 (mtt) cc_final: 0.5457 (mtp) REVERT: D 99 ASP cc_start: 0.4140 (t0) cc_final: 0.3805 (t0) REVERT: D 207 ASP cc_start: 0.5438 (OUTLIER) cc_final: 0.4983 (t0) REVERT: E 26 MET cc_start: 0.5696 (mtt) cc_final: 0.5450 (mtp) REVERT: E 99 ASP cc_start: 0.4138 (t0) cc_final: 0.3801 (t0) REVERT: E 189 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4908 (t80) REVERT: E 207 ASP cc_start: 0.5409 (OUTLIER) cc_final: 0.4926 (t70) REVERT: F 26 MET cc_start: 0.5722 (mtt) cc_final: 0.5461 (mtp) REVERT: F 99 ASP cc_start: 0.4131 (t0) cc_final: 0.3795 (t0) REVERT: F 207 ASP cc_start: 0.5441 (OUTLIER) cc_final: 0.4984 (t0) REVERT: G 26 MET cc_start: 0.5713 (mtt) cc_final: 0.5454 (mtp) REVERT: G 99 ASP cc_start: 0.4144 (t0) cc_final: 0.3809 (t0) REVERT: G 189 TYR cc_start: 0.5133 (OUTLIER) cc_final: 0.4895 (t80) REVERT: G 207 ASP cc_start: 0.5437 (OUTLIER) cc_final: 0.4981 (t0) REVERT: H 26 MET cc_start: 0.5723 (mtt) cc_final: 0.5471 (mtp) REVERT: H 99 ASP cc_start: 0.4145 (t0) cc_final: 0.3810 (t0) REVERT: H 189 TYR cc_start: 0.5088 (OUTLIER) cc_final: 0.4812 (t80) REVERT: H 207 ASP cc_start: 0.5412 (OUTLIER) cc_final: 0.4947 (t0) REVERT: H 308 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.4638 (ttpp) REVERT: I 27 ILE cc_start: 0.4899 (mt) cc_final: 0.4593 (mm) REVERT: I 70 GLU cc_start: 0.4680 (OUTLIER) cc_final: 0.3710 (mp0) REVERT: J 70 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.3706 (mp0) REVERT: K 70 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.3710 (mp0) REVERT: L 70 GLU cc_start: 0.4678 (OUTLIER) cc_final: 0.3745 (mp0) REVERT: M 27 ILE cc_start: 0.4798 (mt) cc_final: 0.4494 (mm) REVERT: M 70 GLU cc_start: 0.4756 (OUTLIER) cc_final: 0.3709 (mp0) REVERT: N 70 GLU cc_start: 0.4756 (OUTLIER) cc_final: 0.3700 (mp0) REVERT: O 70 GLU cc_start: 0.4742 (OUTLIER) cc_final: 0.3700 (mp0) REVERT: P 27 ILE cc_start: 0.4866 (mt) cc_final: 0.4567 (mm) REVERT: P 70 GLU cc_start: 0.4751 (OUTLIER) cc_final: 0.3703 (mp0) REVERT: i 73 TRP cc_start: 0.7244 (OUTLIER) cc_final: 0.6372 (m-90) REVERT: k 73 TRP cc_start: 0.7249 (OUTLIER) cc_final: 0.6426 (m-90) REVERT: j 73 TRP cc_start: 0.7163 (OUTLIER) cc_final: 0.6445 (m-90) REVERT: j 76 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5859 (ttt180) REVERT: l 73 TRP cc_start: 0.7179 (OUTLIER) cc_final: 0.6470 (m-90) outliers start: 64 outliers final: 25 residues processed: 551 average time/residue: 1.8903 time to fit residues: 1220.1245 Evaluate side-chains 550 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 497 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain a residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 2.9990 chunk 450 optimal weight: 10.0000 chunk 411 optimal weight: 8.9990 chunk 438 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 344 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 396 optimal weight: 4.9990 chunk 414 optimal weight: 0.3980 chunk 436 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4643 moved from start: 0.2204 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= 0.254 Angle : 0.672 5.582 55484 Z= 0.363 Chirality : 0.047 0.181 5992 Planarity : 0.005 0.033 7120 Dihedral : 9.949 179.270 5816 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.08 % Allowed : 11.10 % Favored : 87.82 % 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: 0.07 (0.11), residues: 4816 helix: 1.28 (0.12), residues: 1848 sheet: -0.36 (0.17), residues: 784 loop : -0.85 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP h 86 HIS 0.003 0.001 HIS C 310 PHE 0.020 0.002 PHE F 203 TYR 0.016 0.002 TYR G 89 ARG 0.004 0.001 ARG F 315 *********************** 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 546 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 502 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.5657 (mtt) cc_final: 0.5355 (mtp) REVERT: A 123 SER cc_start: 0.4988 (OUTLIER) cc_final: 0.4716 (t) REVERT: A 207 ASP cc_start: 0.5505 (OUTLIER) cc_final: 0.4999 (t70) REVERT: B 26 MET cc_start: 0.5652 (mtt) cc_final: 0.5344 (mtp) REVERT: B 123 SER cc_start: 0.5006 (OUTLIER) cc_final: 0.4735 (t) REVERT: B 189 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4719 (t80) REVERT: B 207 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.4976 (t70) REVERT: C 26 MET cc_start: 0.5629 (mtt) cc_final: 0.5322 (mtp) REVERT: C 123 SER cc_start: 0.4986 (OUTLIER) cc_final: 0.4714 (t) REVERT: C 207 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.4974 (t70) REVERT: D 26 MET cc_start: 0.5674 (mtt) cc_final: 0.5353 (mtp) REVERT: D 123 SER cc_start: 0.5006 (OUTLIER) cc_final: 0.4736 (t) REVERT: D 189 TYR cc_start: 0.4915 (OUTLIER) cc_final: 0.4714 (t80) REVERT: D 207 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.4976 (t70) REVERT: E 26 MET cc_start: 0.5649 (mtt) cc_final: 0.5343 (mtp) REVERT: E 123 SER cc_start: 0.5005 (OUTLIER) cc_final: 0.4732 (t) REVERT: E 189 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4719 (t80) REVERT: E 207 ASP cc_start: 0.5441 (OUTLIER) cc_final: 0.4937 (t70) REVERT: F 26 MET cc_start: 0.5676 (mtt) cc_final: 0.5356 (mtp) REVERT: F 123 SER cc_start: 0.5003 (OUTLIER) cc_final: 0.4732 (t) REVERT: F 189 TYR cc_start: 0.4915 (OUTLIER) cc_final: 0.4714 (t80) REVERT: F 207 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.4975 (t70) REVERT: G 26 MET cc_start: 0.5667 (mtt) cc_final: 0.5345 (mtp) REVERT: G 123 SER cc_start: 0.4988 (OUTLIER) cc_final: 0.4716 (t) REVERT: G 189 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.4718 (t80) REVERT: G 207 ASP cc_start: 0.5470 (OUTLIER) cc_final: 0.4969 (t70) REVERT: H 26 MET cc_start: 0.5658 (mtt) cc_final: 0.5355 (mtp) REVERT: H 123 SER cc_start: 0.5000 (OUTLIER) cc_final: 0.4727 (t) REVERT: H 207 ASP cc_start: 0.5453 (OUTLIER) cc_final: 0.4944 (t70) REVERT: I 27 ILE cc_start: 0.4751 (mt) cc_final: 0.4475 (mm) REVERT: J 27 ILE cc_start: 0.4760 (mt) cc_final: 0.4482 (mm) REVERT: K 27 ILE cc_start: 0.4761 (mt) cc_final: 0.4480 (mm) REVERT: L 27 ILE cc_start: 0.4729 (mt) cc_final: 0.4388 (mm) REVERT: M 27 ILE cc_start: 0.4716 (mt) cc_final: 0.4424 (mm) REVERT: N 27 ILE cc_start: 0.4705 (mt) cc_final: 0.4421 (mm) REVERT: O 27 ILE cc_start: 0.4705 (mt) cc_final: 0.4361 (mm) REVERT: P 27 ILE cc_start: 0.4754 (mt) cc_final: 0.4468 (mm) REVERT: i 73 TRP cc_start: 0.7241 (OUTLIER) cc_final: 0.6364 (m-90) REVERT: k 73 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.6595 (m-90) REVERT: j 73 TRP cc_start: 0.7214 (OUTLIER) cc_final: 0.6486 (m-90) REVERT: j 76 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.5839 (ttt180) REVERT: l 73 TRP cc_start: 0.7426 (OUTLIER) cc_final: 0.6687 (m-90) outliers start: 44 outliers final: 15 residues processed: 539 average time/residue: 1.8958 time to fit residues: 1199.5044 Evaluate side-chains 530 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 489 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain a residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 0.7980 chunk 463 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 486 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4664 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 : 0.006 0.048 40876 Z= 0.360 Angle : 0.807 6.104 55484 Z= 0.435 Chirality : 0.052 0.182 5992 Planarity : 0.006 0.036 7120 Dihedral : 10.224 179.840 5816 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.15 % Allowed : 11.47 % Favored : 87.38 % 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: -0.09 (0.11), residues: 4816 helix: 1.09 (0.12), residues: 1840 sheet: -0.38 (0.17), residues: 776 loop : -0.89 (0.11), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP h 86 HIS 0.004 0.002 HIS D 295 PHE 0.026 0.003 PHE H 203 TYR 0.015 0.003 TYR H 89 ARG 0.008 0.001 ARG D 315 ********************** 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 543 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 496 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: A 26 MET cc_start: 0.5684 (mtt) cc_final: 0.5418 (mtp) REVERT: A 99 ASP cc_start: 0.4088 (t0) cc_final: 0.3726 (t0) REVERT: A 207 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.5028 (t70) REVERT: B 26 MET cc_start: 0.5658 (mtt) cc_final: 0.5395 (mtp) REVERT: B 99 ASP cc_start: 0.4101 (t0) cc_final: 0.3740 (t0) REVERT: B 189 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4821 (t80) REVERT: B 207 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4998 (t70) REVERT: C 26 MET cc_start: 0.5654 (mtt) cc_final: 0.5383 (mtp) REVERT: C 99 ASP cc_start: 0.4096 (t0) cc_final: 0.3735 (t0) REVERT: C 207 ASP cc_start: 0.5503 (OUTLIER) cc_final: 0.5018 (t70) REVERT: C 308 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4585 (ttpp) REVERT: D 26 MET cc_start: 0.5680 (mtt) cc_final: 0.5404 (mtp) REVERT: D 99 ASP cc_start: 0.4110 (t0) cc_final: 0.3755 (t0) REVERT: D 189 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.4788 (t80) REVERT: D 207 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4998 (t70) REVERT: E 26 MET cc_start: 0.5657 (mtt) cc_final: 0.5396 (mtp) REVERT: E 99 ASP cc_start: 0.4117 (t0) cc_final: 0.3760 (t0) REVERT: E 189 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.4840 (t80) REVERT: E 207 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.4964 (t70) REVERT: F 26 MET cc_start: 0.5682 (mtt) cc_final: 0.5407 (mtp) REVERT: F 99 ASP cc_start: 0.4101 (t0) cc_final: 0.3744 (t0) REVERT: F 189 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.4820 (t80) REVERT: F 207 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4996 (t70) REVERT: G 26 MET cc_start: 0.5672 (mtt) cc_final: 0.5397 (mtp) REVERT: G 99 ASP cc_start: 0.4109 (t0) cc_final: 0.3751 (t0) REVERT: G 189 TYR cc_start: 0.5060 (OUTLIER) cc_final: 0.4822 (t80) REVERT: G 207 ASP cc_start: 0.5489 (OUTLIER) cc_final: 0.4994 (t70) REVERT: H 26 MET cc_start: 0.5685 (mtt) cc_final: 0.5419 (mtp) REVERT: H 99 ASP cc_start: 0.4120 (t0) cc_final: 0.3761 (t0) REVERT: H 207 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.4984 (t70) REVERT: I 27 ILE cc_start: 0.4805 (mt) cc_final: 0.4526 (mm) REVERT: J 27 ILE cc_start: 0.4797 (mt) cc_final: 0.4502 (mm) REVERT: J 70 GLU cc_start: 0.4705 (OUTLIER) cc_final: 0.3759 (mp0) REVERT: K 27 ILE cc_start: 0.4796 (mt) cc_final: 0.4505 (mm) REVERT: K 70 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.3762 (mp0) REVERT: M 27 ILE cc_start: 0.4742 (mt) cc_final: 0.4448 (mm) REVERT: M 70 GLU cc_start: 0.4711 (OUTLIER) cc_final: 0.3753 (mp0) REVERT: N 27 ILE cc_start: 0.4756 (mt) cc_final: 0.4458 (mm) REVERT: N 70 GLU cc_start: 0.4714 (OUTLIER) cc_final: 0.3758 (mp0) REVERT: O 27 ILE cc_start: 0.4792 (mt) cc_final: 0.4421 (mm) REVERT: O 70 GLU cc_start: 0.4697 (OUTLIER) cc_final: 0.3746 (mp0) REVERT: P 27 ILE cc_start: 0.4774 (mt) cc_final: 0.4492 (mm) REVERT: i 73 TRP cc_start: 0.7506 (OUTLIER) cc_final: 0.6587 (m-90) REVERT: k 73 TRP cc_start: 0.7495 (OUTLIER) cc_final: 0.6590 (m-90) REVERT: j 73 TRP cc_start: 0.7478 (OUTLIER) cc_final: 0.6672 (m-90) REVERT: j 76 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5844 (ttt180) REVERT: l 73 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.6630 (m-90) outliers start: 47 outliers final: 23 residues processed: 536 average time/residue: 1.8171 time to fit residues: 1149.8392 Evaluate side-chains 542 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 495 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain a residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 7.9990 chunk 412 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 356 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 387 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.137610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.121531 restraints weight = 22350.401| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 0.35 r_work: 0.3054 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work: 0.2876 rms_B_bonded: 2.75 restraints_weight: 0.1250 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 40876 Z= 0.312 Angle : 0.742 5.911 55484 Z= 0.400 Chirality : 0.050 0.180 5992 Planarity : 0.005 0.032 7120 Dihedral : 10.108 179.825 5816 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.27 % Allowed : 11.62 % Favored : 87.11 % 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: 1.18 (0.12), residues: 1840 sheet: -0.40 (0.17), residues: 784 loop : -0.88 (0.11), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP h 86 HIS 0.004 0.001 HIS G 295 PHE 0.023 0.002 PHE F 203 TYR 0.014 0.002 TYR G 89 ARG 0.013 0.001 ARG G 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18383.83 seconds wall clock time: 323 minutes 44.90 seconds (19424.90 seconds total)