Starting phenix.real_space_refine on Sun Mar 24 08:57:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpu_7973/03_2024/6dpu_7973_updated.pdb" } resolution = 3.1 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= -0.007 sd= 0.929 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 282 5.16 5 C 25542 2.51 5 N 6936 2.21 5 O 7842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 320": "NH1" <-> "NH2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "I GLU 160": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J GLU 279": "OE1" <-> "OE2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 320": "NH1" <-> "NH2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 320": "NH1" <-> "NH2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40650 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.33, per 1000 atoms: 0.50 Number of scatterers: 40650 At special positions: 0 Unit cell: (173.168, 85.488, 212.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 36 15.00 Mg 12 11.99 O 7842 8.00 N 6936 7.00 C 25542 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: 16.27 Conformation dependent library (CDL) restraints added in 7.1 seconds 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 30 sheets defined 50.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.612A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.573A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.095A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.561A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 197 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.439A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.674A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.686A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.547A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.553A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.376A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.566A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.806A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.627A pdb=" N ARG B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.612A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.573A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.094A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.561A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.439A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.674A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.685A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.545A pdb=" N TYR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.376A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.809A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.633A pdb=" N ARG D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 436 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.611A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.572A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.095A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.561A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS E 197 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.440A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.673A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 283' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.687A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.547A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.375A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.807A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 3.632A pdb=" N ARG F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 Processing helix chain 'F' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.375A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.805A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 3.633A pdb=" N ARG G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 Processing helix chain 'G' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.376A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.806A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 279 through 281 No H-bonds generated for 'chain 'H' and resid 279 through 281' Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.633A pdb=" N ARG H 390 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 Processing helix chain 'H' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.376A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 3.806A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 279 through 281 No H-bonds generated for 'chain 'I' and resid 279 through 281' Processing helix chain 'I' and resid 288 through 296 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 3.634A pdb=" N ARG I 390 " --> pdb=" O LEU I 387 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 Processing helix chain 'I' and resid 415 through 436 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.610A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.573A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.094A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.558A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS J 197 " --> pdb=" O THR J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.439A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.671A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 283' Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.688A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.547A pdb=" N TYR J 399 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.611A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.573A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.094A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.559A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS K 197 " --> pdb=" O THR K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.439A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.672A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 278 through 283' Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.686A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.547A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.611A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.573A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.094A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.559A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS L 197 " --> pdb=" O THR L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.438A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.673A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 283' Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.686A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.546A pdb=" N TYR L 399 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.979A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.980A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.981A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP G 205 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE G 272 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.982A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP H 205 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE H 272 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.982A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP I 205 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE I 272 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.981A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= AD, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) 1817 hydrogen bonds defined for protein. 4659 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: 16.91 Time building geometry restraints manager: 17.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7421 1.32 - 1.45: 10794 1.45 - 1.57: 22838 1.57 - 1.69: 65 1.69 - 1.81: 456 Bond restraints: 41574 Sorted by residual: bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.605 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.612 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 41569 not shown) Histogram of bond angle deviations from ideal: 94.83 - 103.30: 497 103.30 - 111.78: 16615 111.78 - 120.25: 22139 120.25 - 128.72: 16905 128.72 - 137.19: 334 Bond angle restraints: 56490 Sorted by residual: angle pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" O2' G2P B 501 " ideal model delta sigma weight residual 116.29 100.29 16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" N THR L 73 " pdb=" CA THR L 73 " pdb=" C THR L 73 " ideal model delta sigma weight residual 111.11 117.50 -6.39 1.20e+00 6.94e-01 2.84e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.49 -6.38 1.20e+00 6.94e-01 2.83e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.49 -6.38 1.20e+00 6.94e-01 2.82e+01 angle pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" O2' G2P D 501 " ideal model delta sigma weight residual 116.29 100.38 15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 56485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 23946 33.70 - 67.41: 804 67.41 - 101.11: 54 101.11 - 134.81: 0 134.81 - 168.52: 18 Dihedral angle restraints: 24822 sinusoidal: 9966 harmonic: 14856 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.21 -168.52 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.60 -168.13 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.67 -168.07 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4429 0.085 - 0.169: 1372 0.169 - 0.254: 301 0.254 - 0.338: 70 0.338 - 0.423: 2 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" C4' G2P D 501 " pdb=" O3' G2P D 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.29 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA LEU L 269 " pdb=" N LEU L 269 " pdb=" C LEU L 269 " pdb=" CB LEU L 269 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 6171 not shown) Planarity restraints: 7350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.025 2.00e-02 2.50e+03 1.21e-02 4.39e+00 pdb=" C2 GTP C 501 " -0.010 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.009 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.025 2.00e-02 2.50e+03 1.20e-02 4.33e+00 pdb=" C2 GTP L 501 " -0.007 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.031 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP K 501 " -0.023 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" C2 GTP K 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP K 501 " -0.005 2.00e-02 2.50e+03 pdb=" C8 GTP K 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 GTP K 501 " -0.007 2.00e-02 2.50e+03 pdb=" N2 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP K 501 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" N9 GTP K 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP K 501 " -0.003 2.00e-02 2.50e+03 ... (remaining 7347 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 69 2.51 - 3.11: 28599 3.11 - 3.71: 64641 3.71 - 4.30: 93413 4.30 - 4.90: 158805 Nonbonded interactions: 345527 Sorted by model distance: nonbonded pdb=" O3G GTP J 501 " pdb="MG MG J 502 " model vdw 1.913 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.960 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.969 2.170 nonbonded pdb=" O3G GTP E 501 " pdb="MG MG E 502 " model vdw 1.971 2.170 nonbonded pdb=" O2B G2P G 501 " pdb="MG MG G 502 " model vdw 1.972 2.170 ... (remaining 345522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 6.580 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: 0.050 Extract box with map and model: 29.770 Check model and map are aligned: 0.630 Set scattering table: 0.350 Process input model: 106.680 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.410 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 41574 Z= 0.607 Angle : 1.532 16.001 56490 Z= 1.036 Chirality : 0.087 0.423 6174 Planarity : 0.006 0.055 7350 Dihedral : 16.460 168.516 15294 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 3.17 % Allowed : 8.26 % Favored : 88.57 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5106 helix: 0.72 (0.09), residues: 2334 sheet: 0.55 (0.18), residues: 792 loop : -1.18 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP L 21 HIS 0.007 0.002 HIS C 88 PHE 0.026 0.003 PHE F 92 TYR 0.022 0.003 TYR D 224 ARG 0.026 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1546 time to evaluate : 4.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7989 (ttmt) REVERT: D 5 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7625 (t) REVERT: D 120 ASP cc_start: 0.7444 (m-30) cc_final: 0.7189 (m-30) REVERT: D 306 ASP cc_start: 0.6300 (t0) cc_final: 0.5981 (t0) REVERT: E 91 GLN cc_start: 0.7347 (mt0) cc_final: 0.6885 (mt0) REVERT: E 110 ILE cc_start: 0.8835 (mm) cc_final: 0.8602 (mm) REVERT: E 280 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7935 (ttmt) REVERT: G 156 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8140 (mmtt) REVERT: G 414 ASP cc_start: 0.7440 (t0) cc_final: 0.7043 (m-30) REVERT: G 435 TYR cc_start: 0.7432 (m-80) cc_final: 0.7067 (m-80) REVERT: H 156 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8200 (mmtt) REVERT: H 199 ASP cc_start: 0.7570 (m-30) cc_final: 0.7364 (m-30) REVERT: H 300 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (t0) REVERT: H 325 MET cc_start: 0.7600 (mmm) cc_final: 0.7164 (mmm) REVERT: H 414 ASP cc_start: 0.7171 (t0) cc_final: 0.6849 (m-30) REVERT: H 426 ASN cc_start: 0.7797 (m-40) cc_final: 0.7561 (m110) REVERT: H 435 TYR cc_start: 0.7387 (m-80) cc_final: 0.7073 (m-10) REVERT: I 207 GLU cc_start: 0.6914 (tt0) cc_final: 0.6517 (tt0) REVERT: I 283 TYR cc_start: 0.8274 (m-80) cc_final: 0.7874 (m-80) REVERT: I 306 ASP cc_start: 0.6456 (t0) cc_final: 0.5907 (t70) REVERT: I 426 ASN cc_start: 0.7913 (m-40) cc_final: 0.7465 (m110) REVERT: J 91 GLN cc_start: 0.7425 (mt0) cc_final: 0.7103 (mt0) REVERT: J 123 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6888 (ttp-110) REVERT: K 120 ASP cc_start: 0.5999 (t0) cc_final: 0.5683 (t0) REVERT: K 123 ARG cc_start: 0.7037 (ttp-110) cc_final: 0.6786 (ttp-110) REVERT: L 209 ILE cc_start: 0.8583 (mm) cc_final: 0.7919 (mp) REVERT: L 302 MET cc_start: 0.7787 (mmp) cc_final: 0.7162 (mmt) outliers start: 138 outliers final: 32 residues processed: 1633 average time/residue: 0.5628 time to fit residues: 1455.5742 Evaluate side-chains 849 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 815 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 300 ASN Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 192 HIS Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 3.9990 chunk 386 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 399 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 463 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 228 ASN A 258 ASN A 300 ASN B 6 HIS B 28 HIS B 37 HIS B 85 GLN B 101 ASN B 133 GLN B 136 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 101 ASN C 107 HIS C 228 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS D 28 HIS D 101 ASN D 133 GLN D 136 GLN D 385 GLN D 436 GLN E 101 ASN E 107 HIS E 216 ASN E 228 ASN E 258 ASN E 300 ASN F 6 HIS F 28 HIS F 37 HIS F 85 GLN F 101 ASN F 133 GLN F 136 GLN F 300 ASN F 309 HIS F 349 ASN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 133 GLN G 136 GLN G 247 GLN G 436 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 85 GLN H 133 GLN H 136 GLN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 436 GLN I 6 HIS I 28 HIS I 133 GLN I 136 GLN I 247 GLN I 300 ASN I 434 GLN I 436 GLN J 101 ASN J 107 HIS J 133 GLN J 228 ASN J 300 ASN K 18 ASN K 91 GLN K 107 HIS K 133 GLN K 226 ASN K 228 ASN K 300 ASN L 18 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 228 ASN L 256 GLN L 300 ASN L 380 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 41574 Z= 0.302 Angle : 0.622 7.381 56490 Z= 0.329 Chirality : 0.046 0.203 6174 Planarity : 0.005 0.055 7350 Dihedral : 12.625 175.260 5903 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.67 % Allowed : 14.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 5106 helix: 1.59 (0.10), residues: 2352 sheet: 0.57 (0.17), residues: 774 loop : -0.94 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 346 HIS 0.015 0.002 HIS F 309 PHE 0.027 0.002 PHE E 255 TYR 0.016 0.002 TYR H 283 ARG 0.006 0.001 ARG K 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 858 time to evaluate : 4.809 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 66 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 290 GLU cc_start: 0.5525 (mt-10) cc_final: 0.5240 (mt-10) REVERT: B 120 ASP cc_start: 0.7127 (m-30) cc_final: 0.6836 (m-30) REVERT: C 327 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7311 (p0) REVERT: E 75 ILE cc_start: 0.8949 (mm) cc_final: 0.8622 (mm) REVERT: E 91 GLN cc_start: 0.7708 (mt0) cc_final: 0.7369 (mt0) REVERT: G 24 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8529 (tt) REVERT: G 435 TYR cc_start: 0.7119 (m-80) cc_final: 0.6916 (m-10) REVERT: H 31 ASP cc_start: 0.7515 (p0) cc_final: 0.7308 (p0) REVERT: H 207 GLU cc_start: 0.6728 (tt0) cc_final: 0.6512 (tt0) REVERT: H 325 MET cc_start: 0.7445 (mmm) cc_final: 0.7173 (mmm) REVERT: H 422 GLU cc_start: 0.7642 (tp30) cc_final: 0.7372 (tp30) REVERT: H 435 TYR cc_start: 0.7098 (m-80) cc_final: 0.6635 (m-10) REVERT: I 207 GLU cc_start: 0.6698 (tt0) cc_final: 0.6450 (tt0) REVERT: I 211 ASP cc_start: 0.7503 (m-30) cc_final: 0.7262 (m-30) REVERT: I 283 TYR cc_start: 0.8252 (m-80) cc_final: 0.7971 (m-80) REVERT: I 422 GLU cc_start: 0.7737 (tp30) cc_final: 0.7089 (tp30) REVERT: I 426 ASN cc_start: 0.7887 (m-40) cc_final: 0.7330 (m110) REVERT: K 120 ASP cc_start: 0.6163 (t0) cc_final: 0.5903 (t0) REVERT: L 413 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7675 (mtp) outliers start: 160 outliers final: 87 residues processed: 961 average time/residue: 0.5213 time to fit residues: 812.2275 Evaluate side-chains 794 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 703 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 192 HIS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 385 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 463 optimal weight: 5.9990 chunk 501 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 433 GLN B 436 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 18 ASN F 50 ASN F 385 GLN F 436 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 37 HIS H 50 ASN H 133 GLN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 50 ASN I 133 GLN I 349 ASN J 226 ASN J 300 ASN K 128 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 256 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41574 Z= 0.279 Angle : 0.575 9.050 56490 Z= 0.298 Chirality : 0.044 0.177 6174 Planarity : 0.005 0.046 7350 Dihedral : 12.292 178.359 5890 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.93 % Allowed : 15.70 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.12), residues: 5106 helix: 1.49 (0.11), residues: 2358 sheet: 0.52 (0.18), residues: 774 loop : -0.91 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 346 HIS 0.008 0.001 HIS C 88 PHE 0.030 0.002 PHE K 255 TYR 0.016 0.002 TYR H 283 ARG 0.007 0.001 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 764 time to evaluate : 4.147 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 66 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 120 ASP cc_start: 0.7185 (m-30) cc_final: 0.6890 (m-30) REVERT: B 352 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.6988 (tmtt) REVERT: C 327 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7316 (p0) REVERT: D 94 PHE cc_start: 0.8421 (p90) cc_final: 0.8192 (p90) REVERT: E 84 ARG cc_start: 0.7779 (ptt-90) cc_final: 0.7558 (ptt-90) REVERT: E 110 ILE cc_start: 0.8915 (mm) cc_final: 0.8674 (mm) REVERT: F 116 ASP cc_start: 0.6974 (m-30) cc_final: 0.6704 (m-30) REVERT: F 301 MET cc_start: 0.8097 (mmp) cc_final: 0.7727 (mmp) REVERT: G 24 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8586 (tt) REVERT: G 435 TYR cc_start: 0.6982 (m-80) cc_final: 0.6779 (m-10) REVERT: H 191 VAL cc_start: 0.8561 (t) cc_final: 0.8282 (t) REVERT: I 211 ASP cc_start: 0.7522 (m-30) cc_final: 0.7267 (m-30) REVERT: I 398 MET cc_start: 0.7542 (mtm) cc_final: 0.7328 (mtm) REVERT: I 422 GLU cc_start: 0.7689 (tp30) cc_final: 0.6965 (tp30) REVERT: I 426 ASN cc_start: 0.7841 (m-40) cc_final: 0.7155 (m110) REVERT: L 413 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7807 (mtp) outliers start: 171 outliers final: 115 residues processed: 874 average time/residue: 0.5189 time to fit residues: 741.2701 Evaluate side-chains 797 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 677 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 192 HIS Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 0.9990 chunk 348 optimal weight: 10.0000 chunk 240 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 311 optimal weight: 2.9990 chunk 465 optimal weight: 6.9990 chunk 492 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 441 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 309 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 247 GLN D 293 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS H 309 HIS I 349 ASN J 31 GLN K 128 GLN K 133 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41574 Z= 0.220 Angle : 0.528 7.351 56490 Z= 0.273 Chirality : 0.042 0.144 6174 Planarity : 0.004 0.046 7350 Dihedral : 12.097 176.193 5887 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.76 % Allowed : 16.87 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 5106 helix: 1.44 (0.11), residues: 2316 sheet: 0.57 (0.18), residues: 774 loop : -0.90 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 346 HIS 0.013 0.001 HIS B 309 PHE 0.029 0.002 PHE E 255 TYR 0.015 0.001 TYR G 185 ARG 0.007 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 734 time to evaluate : 4.668 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: B 120 ASP cc_start: 0.7130 (m-30) cc_final: 0.6891 (m-30) REVERT: B 352 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.6920 (tmtt) REVERT: D 413 MET cc_start: 0.7649 (mtp) cc_final: 0.7409 (ttm) REVERT: E 75 ILE cc_start: 0.8777 (mm) cc_final: 0.8353 (mm) REVERT: E 84 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7571 (ptt-90) REVERT: E 302 MET cc_start: 0.7519 (mmm) cc_final: 0.7025 (mmm) REVERT: F 301 MET cc_start: 0.8058 (mmp) cc_final: 0.7599 (mmp) REVERT: G 24 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8673 (tt) REVERT: H 24 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8687 (tt) REVERT: H 133 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: H 308 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7418 (mtm180) REVERT: I 211 ASP cc_start: 0.7446 (m-30) cc_final: 0.7182 (m-30) REVERT: I 422 GLU cc_start: 0.7723 (tp30) cc_final: 0.7028 (tp30) REVERT: I 425 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7344 (ttt) REVERT: I 426 ASN cc_start: 0.7872 (m-40) cc_final: 0.7181 (m110) REVERT: J 214 ARG cc_start: 0.7244 (tmm160) cc_final: 0.6993 (ttp-170) REVERT: L 413 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7797 (mtp) outliers start: 164 outliers final: 124 residues processed: 839 average time/residue: 0.5320 time to fit residues: 738.6219 Evaluate side-chains 786 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 656 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 215 ARG Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 367 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 420 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 0.7980 chunk 442 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 ASN H 229 HIS I 309 HIS K 256 GLN K 406 HIS L 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41574 Z= 0.242 Angle : 0.530 8.126 56490 Z= 0.273 Chirality : 0.042 0.137 6174 Planarity : 0.004 0.047 7350 Dihedral : 12.007 175.542 5886 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.57 % Allowed : 17.06 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 5106 helix: 1.26 (0.11), residues: 2376 sheet: 0.63 (0.18), residues: 798 loop : -0.96 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 346 HIS 0.008 0.001 HIS B 309 PHE 0.028 0.002 PHE E 255 TYR 0.019 0.001 TYR G 435 ARG 0.007 0.000 ARG K 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 705 time to evaluate : 4.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.7169 (m-30) cc_final: 0.6905 (m-30) REVERT: B 308 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7367 (mtm110) REVERT: B 352 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7169 (tmtt) REVERT: D 165 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (mm) REVERT: E 75 ILE cc_start: 0.8841 (mm) cc_final: 0.8413 (mm) REVERT: F 299 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7824 (mtpt) REVERT: F 301 MET cc_start: 0.8113 (mmp) cc_final: 0.7673 (mmp) REVERT: H 133 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6840 (pt0) REVERT: H 207 GLU cc_start: 0.6799 (tt0) cc_final: 0.6556 (tt0) REVERT: H 308 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7331 (mtm180) REVERT: I 211 ASP cc_start: 0.7463 (m-30) cc_final: 0.7222 (m-30) REVERT: I 422 GLU cc_start: 0.7766 (tp30) cc_final: 0.7038 (tp30) REVERT: I 426 ASN cc_start: 0.7902 (m-40) cc_final: 0.7189 (m110) REVERT: J 214 ARG cc_start: 0.7241 (tmm160) cc_final: 0.7021 (ttp-170) REVERT: L 88 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5936 (p90) REVERT: L 93 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7969 (mt) REVERT: L 413 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7870 (mtp) outliers start: 199 outliers final: 145 residues processed: 835 average time/residue: 0.5042 time to fit residues: 694.3179 Evaluate side-chains 815 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 664 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 10.0000 chunk 443 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 493 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 163 optimal weight: 0.0870 chunk 259 optimal weight: 6.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN G 6 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS H 229 HIS H 309 HIS K 256 GLN L 256 GLN L 406 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 41574 Z= 0.242 Angle : 0.528 6.699 56490 Z= 0.272 Chirality : 0.042 0.144 6174 Planarity : 0.004 0.050 7350 Dihedral : 11.914 174.415 5880 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.36 % Allowed : 17.36 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 5106 helix: 1.19 (0.11), residues: 2364 sheet: 0.62 (0.18), residues: 798 loop : -0.96 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 346 HIS 0.008 0.001 HIS B 309 PHE 0.028 0.002 PHE E 255 TYR 0.013 0.001 TYR I 435 ARG 0.005 0.000 ARG K 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 700 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.7153 (m-30) cc_final: 0.6898 (m-30) REVERT: B 352 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7166 (tmtt) REVERT: E 75 ILE cc_start: 0.8838 (mm) cc_final: 0.8397 (mm) REVERT: F 301 MET cc_start: 0.8103 (mmp) cc_final: 0.7663 (mmp) REVERT: H 133 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6874 (pt0) REVERT: H 264 ARG cc_start: 0.7107 (mmm-85) cc_final: 0.6835 (mmm160) REVERT: I 207 GLU cc_start: 0.6935 (tt0) cc_final: 0.6479 (tt0) REVERT: I 211 ASP cc_start: 0.7431 (m-30) cc_final: 0.7162 (m-30) REVERT: I 422 GLU cc_start: 0.7861 (tp30) cc_final: 0.7272 (tp30) REVERT: I 426 ASN cc_start: 0.7906 (m-40) cc_final: 0.7195 (m110) REVERT: L 88 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.5925 (p90) REVERT: L 413 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (mtp) outliers start: 190 outliers final: 153 residues processed: 828 average time/residue: 0.5158 time to fit residues: 704.2274 Evaluate side-chains 812 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 655 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 281 optimal weight: 0.9990 chunk 360 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 415 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 491 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 HIS L 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 41574 Z= 0.159 Angle : 0.495 7.369 56490 Z= 0.254 Chirality : 0.041 0.141 6174 Planarity : 0.004 0.046 7350 Dihedral : 11.659 171.662 5878 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.40 % Allowed : 18.71 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.12), residues: 5106 helix: 1.26 (0.11), residues: 2364 sheet: 0.76 (0.18), residues: 852 loop : -0.90 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 346 HIS 0.006 0.001 HIS B 309 PHE 0.025 0.001 PHE E 255 TYR 0.013 0.001 TYR G 283 ARG 0.009 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 731 time to evaluate : 4.687 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: B 120 ASP cc_start: 0.7097 (m-30) cc_final: 0.6836 (m-30) REVERT: B 166 MET cc_start: 0.7922 (tpt) cc_final: 0.7718 (tpp) REVERT: B 308 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7467 (mtm110) REVERT: B 352 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6911 (tmtt) REVERT: D 308 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7515 (mtm110) REVERT: D 413 MET cc_start: 0.7842 (mtp) cc_final: 0.7608 (ttm) REVERT: E 75 ILE cc_start: 0.8714 (mm) cc_final: 0.8285 (mm) REVERT: F 301 MET cc_start: 0.8059 (mmp) cc_final: 0.7639 (mmp) REVERT: H 133 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: H 264 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6867 (mmm160) REVERT: H 323 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7116 (ptp) REVERT: I 211 ASP cc_start: 0.7472 (m-30) cc_final: 0.7177 (m-30) REVERT: I 422 GLU cc_start: 0.7891 (tp30) cc_final: 0.7316 (tp30) REVERT: I 426 ASN cc_start: 0.7904 (m-40) cc_final: 0.7192 (m110) REVERT: J 195 LEU cc_start: 0.8103 (mt) cc_final: 0.7842 (mt) REVERT: L 88 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5736 (p90) REVERT: L 93 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7973 (mt) REVERT: L 128 GLN cc_start: 0.7866 (tt0) cc_final: 0.7633 (tt0) REVERT: L 413 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7849 (mtp) outliers start: 148 outliers final: 112 residues processed: 818 average time/residue: 0.5174 time to fit residues: 693.6511 Evaluate side-chains 801 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 683 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 312 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 386 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS H 434 GLN I 229 HIS J 31 GLN L 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41574 Z= 0.244 Angle : 0.534 7.160 56490 Z= 0.274 Chirality : 0.042 0.144 6174 Planarity : 0.004 0.052 7350 Dihedral : 11.685 171.312 5876 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.70 % Allowed : 18.69 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5106 helix: 1.19 (0.11), residues: 2358 sheet: 0.68 (0.18), residues: 852 loop : -0.97 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 346 HIS 0.007 0.001 HIS B 309 PHE 0.025 0.002 PHE E 255 TYR 0.014 0.001 TYR I 185 ARG 0.008 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 673 time to evaluate : 5.382 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 35 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7798 (mm110) REVERT: B 120 ASP cc_start: 0.7147 (m-30) cc_final: 0.6887 (m-30) REVERT: B 352 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7167 (tmtt) REVERT: D 413 MET cc_start: 0.7887 (mtp) cc_final: 0.7631 (ttm) REVERT: F 301 MET cc_start: 0.8044 (mmp) cc_final: 0.7615 (mmp) REVERT: H 133 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7058 (pt0) REVERT: H 264 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6939 (mmm160) REVERT: H 323 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7258 (ptp) REVERT: I 211 ASP cc_start: 0.7423 (m-30) cc_final: 0.7153 (m-30) REVERT: I 422 GLU cc_start: 0.7924 (tp30) cc_final: 0.7351 (tp30) REVERT: I 426 ASN cc_start: 0.7910 (m-40) cc_final: 0.7189 (m110) REVERT: K 110 ILE cc_start: 0.9039 (mm) cc_final: 0.8732 (mm) REVERT: L 88 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.5947 (p90) REVERT: L 93 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7939 (mt) REVERT: L 413 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7968 (mtp) outliers start: 161 outliers final: 133 residues processed: 776 average time/residue: 0.5047 time to fit residues: 647.4852 Evaluate side-chains 792 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 653 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 3.9990 chunk 470 optimal weight: 0.0020 chunk 429 optimal weight: 0.0040 chunk 458 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 413 optimal weight: 6.9990 chunk 433 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS I 229 HIS I 309 HIS K 101 ASN L 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41574 Z= 0.290 Angle : 0.557 7.689 56490 Z= 0.286 Chirality : 0.043 0.146 6174 Planarity : 0.005 0.056 7350 Dihedral : 11.718 171.644 5873 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.74 % Allowed : 18.96 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 5106 helix: 1.04 (0.11), residues: 2364 sheet: 0.56 (0.18), residues: 852 loop : -1.03 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 346 HIS 0.006 0.001 HIS K 88 PHE 0.029 0.002 PHE L 255 TYR 0.018 0.001 TYR H 435 ARG 0.008 0.001 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 682 time to evaluate : 4.633 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 35 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7793 (mm110) REVERT: A 425 MET cc_start: 0.7718 (tpp) cc_final: 0.7452 (tpt) REVERT: B 120 ASP cc_start: 0.7183 (m-30) cc_final: 0.6917 (m-30) REVERT: B 308 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7384 (mtm110) REVERT: B 352 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7178 (tmtt) REVERT: D 308 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7658 (mtm110) REVERT: D 413 MET cc_start: 0.8001 (mtp) cc_final: 0.7762 (ttm) REVERT: E 75 ILE cc_start: 0.8785 (mm) cc_final: 0.8468 (mm) REVERT: F 301 MET cc_start: 0.8041 (mmp) cc_final: 0.7722 (mmp) REVERT: H 264 ARG cc_start: 0.7320 (mmm-85) cc_final: 0.7024 (mmm160) REVERT: I 211 ASP cc_start: 0.7445 (m-30) cc_final: 0.7175 (m-30) REVERT: I 422 GLU cc_start: 0.7960 (tp30) cc_final: 0.7398 (tp30) REVERT: I 426 ASN cc_start: 0.7926 (m-40) cc_final: 0.7201 (m110) REVERT: K 110 ILE cc_start: 0.9073 (mm) cc_final: 0.8777 (mm) REVERT: L 88 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6053 (p90) REVERT: L 93 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7948 (mt) outliers start: 163 outliers final: 140 residues processed: 790 average time/residue: 0.5199 time to fit residues: 679.4848 Evaluate side-chains 802 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 659 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 0.0270 chunk 484 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 508 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 HIS ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 HIS ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41574 Z= 0.232 Angle : 0.541 9.923 56490 Z= 0.277 Chirality : 0.042 0.145 6174 Planarity : 0.004 0.055 7350 Dihedral : 11.640 171.274 5873 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.40 % Allowed : 19.49 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 5106 helix: 1.07 (0.11), residues: 2364 sheet: 0.57 (0.18), residues: 852 loop : -1.04 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 346 HIS 0.007 0.001 HIS B 309 PHE 0.031 0.001 PHE L 255 TYR 0.015 0.001 TYR H 435 ARG 0.008 0.000 ARG G 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 682 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7804 (mm110) REVERT: A 425 MET cc_start: 0.7734 (tpp) cc_final: 0.7463 (tpt) REVERT: B 120 ASP cc_start: 0.7167 (m-30) cc_final: 0.6910 (m-30) REVERT: B 308 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7300 (mtm110) REVERT: B 352 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7133 (tmtt) REVERT: D 413 MET cc_start: 0.7967 (mtp) cc_final: 0.7750 (ttm) REVERT: E 75 ILE cc_start: 0.8704 (mm) cc_final: 0.8382 (mm) REVERT: F 301 MET cc_start: 0.8036 (mmp) cc_final: 0.7675 (mmp) REVERT: H 264 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.7055 (mmm160) REVERT: I 211 ASP cc_start: 0.7430 (m-30) cc_final: 0.7163 (m-30) REVERT: I 422 GLU cc_start: 0.7958 (tp30) cc_final: 0.7416 (tp30) REVERT: I 426 ASN cc_start: 0.7920 (m-40) cc_final: 0.7198 (m110) REVERT: K 110 ILE cc_start: 0.9042 (mm) cc_final: 0.8751 (mm) REVERT: L 88 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.5981 (p90) REVERT: L 93 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7933 (mt) outliers start: 148 outliers final: 139 residues processed: 778 average time/residue: 0.5125 time to fit residues: 656.0406 Evaluate side-chains 797 residues out of total 4392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 655 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 405 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 416 optimal weight: 0.0060 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 59 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN G 197 ASN ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 HIS I 309 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109358 restraints weight = 51491.538| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.95 r_work: 0.3393 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41574 Z= 0.201 Angle : 0.521 8.573 56490 Z= 0.267 Chirality : 0.042 0.143 6174 Planarity : 0.004 0.054 7350 Dihedral : 11.511 170.122 5873 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.28 % Allowed : 19.86 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 5106 helix: 1.13 (0.11), residues: 2358 sheet: 0.63 (0.18), residues: 852 loop : -1.01 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 346 HIS 0.007 0.001 HIS C 88 PHE 0.030 0.001 PHE L 255 TYR 0.013 0.001 TYR H 435 ARG 0.011 0.000 ARG G 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12735.97 seconds wall clock time: 228 minutes 9.14 seconds (13689.14 seconds total)