Starting phenix.real_space_refine on Tue Apr 16 12:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/04_2024/7u5h_26350.pdb" } resolution = 3.32 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= 0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 24 6.06 5 S 204 5.16 5 C 24816 2.51 5 N 6960 2.21 5 O 7188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "H GLU 297": "OE1" <-> "OE2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "J GLU 297": "OE1" <-> "OE2" Residue "K GLU 297": "OE1" <-> "OE2" Residue "L GLU 297": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39192 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "C" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "D" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "E" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "F" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "G" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "H" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "I" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "J" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "K" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "L" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.24, per 1000 atoms: 0.52 Number of scatterers: 39192 At special positions: 0 Unit cell: (157.29, 153.01, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 24 29.99 S 204 16.00 O 7188 8.00 N 6960 7.00 C 24816 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: 14.88 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 436 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 90 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 436 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 90 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 436 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 90 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 436 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 90 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 436 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 90 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 436 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 90 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 436 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 90 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 436 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 90 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" NE2 HIS I 436 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 90 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" NE2 HIS J 436 " pdb=" ZN J 502 " pdb="ZN ZN J 502 " - pdb=" NE2 HIS J 90 " pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" NE2 HIS K 436 " pdb=" ZN K 502 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 90 " pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" NE2 HIS L 436 " pdb=" ZN L 502 " pdb="ZN ZN L 502 " - pdb=" NE2 HIS L 90 " 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9528 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 38.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 23 Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 327 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 284 removed outlier: 4.068A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 327 through 336 Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 444 through 466 removed outlier: 4.278A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Proline residue: B 462 - end of helix Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 327 through 336 Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 444 through 466 removed outlier: 4.278A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Proline residue: C 462 - end of helix Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 189 through 196 Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 327 through 336 Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'E' and resid 7 through 23 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 214 through 225 Processing helix chain 'E' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA E 278 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 327 through 336 Proline residue: E 334 - end of helix Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU E 448 " --> pdb=" O THR E 444 " (cutoff:3.500A) Proline residue: E 462 - end of helix Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 214 through 225 Processing helix chain 'F' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA F 278 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 327 through 336 Proline residue: F 334 - end of helix Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 413 through 422 Processing helix chain 'F' and resid 444 through 466 removed outlier: 4.280A pdb=" N LEU F 448 " --> pdb=" O THR F 444 " (cutoff:3.500A) Proline residue: F 462 - end of helix Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 189 through 196 Processing helix chain 'G' and resid 214 through 225 Processing helix chain 'G' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA G 278 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU G 282 " --> pdb=" O ALA G 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 310 through 321 Processing helix chain 'G' and resid 327 through 336 Proline residue: G 334 - end of helix Processing helix chain 'G' and resid 380 through 395 Processing helix chain 'G' and resid 413 through 422 Processing helix chain 'G' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU G 448 " --> pdb=" O THR G 444 " (cutoff:3.500A) Proline residue: G 462 - end of helix Processing helix chain 'H' and resid 7 through 23 Processing helix chain 'H' and resid 26 through 40 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 189 through 196 Processing helix chain 'H' and resid 214 through 225 Processing helix chain 'H' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA H 278 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU H 282 " --> pdb=" O ALA H 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 300 Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 327 through 336 Proline residue: H 334 - end of helix Processing helix chain 'H' and resid 380 through 395 Processing helix chain 'H' and resid 413 through 422 Processing helix chain 'H' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU H 448 " --> pdb=" O THR H 444 " (cutoff:3.500A) Proline residue: H 462 - end of helix Processing helix chain 'I' and resid 7 through 23 Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 189 through 196 Processing helix chain 'I' and resid 214 through 225 Processing helix chain 'I' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA I 278 " --> pdb=" O ASP I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 300 Processing helix chain 'I' and resid 310 through 321 Processing helix chain 'I' and resid 327 through 336 Proline residue: I 334 - end of helix Processing helix chain 'I' and resid 380 through 395 Processing helix chain 'I' and resid 413 through 422 Processing helix chain 'I' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU I 448 " --> pdb=" O THR I 444 " (cutoff:3.500A) Proline residue: I 462 - end of helix Processing helix chain 'J' and resid 7 through 23 Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 179 through 183 Processing helix chain 'J' and resid 189 through 196 Processing helix chain 'J' and resid 214 through 225 Processing helix chain 'J' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA J 278 " --> pdb=" O ASP J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 284 removed outlier: 4.068A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 300 Processing helix chain 'J' and resid 310 through 321 Processing helix chain 'J' and resid 327 through 336 Proline residue: J 334 - end of helix Processing helix chain 'J' and resid 380 through 395 Processing helix chain 'J' and resid 413 through 422 Processing helix chain 'J' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU J 448 " --> pdb=" O THR J 444 " (cutoff:3.500A) Proline residue: J 462 - end of helix Processing helix chain 'K' and resid 7 through 23 Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 189 through 196 Processing helix chain 'K' and resid 214 through 225 Processing helix chain 'K' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA K 278 " --> pdb=" O ASP K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 300 Processing helix chain 'K' and resid 310 through 321 Processing helix chain 'K' and resid 327 through 336 Proline residue: K 334 - end of helix Processing helix chain 'K' and resid 380 through 395 Processing helix chain 'K' and resid 413 through 422 Processing helix chain 'K' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU K 448 " --> pdb=" O THR K 444 " (cutoff:3.500A) Proline residue: K 462 - end of helix Processing helix chain 'L' and resid 7 through 23 Processing helix chain 'L' and resid 26 through 40 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 179 through 183 Processing helix chain 'L' and resid 189 through 196 Processing helix chain 'L' and resid 214 through 225 Processing helix chain 'L' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA L 278 " --> pdb=" O ASP L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA L 284 " --> pdb=" O ALA L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 300 Processing helix chain 'L' and resid 310 through 321 Processing helix chain 'L' and resid 327 through 336 Proline residue: L 334 - end of helix Processing helix chain 'L' and resid 380 through 395 Processing helix chain 'L' and resid 413 through 422 Processing helix chain 'L' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU L 448 " --> pdb=" O THR L 444 " (cutoff:3.500A) Proline residue: L 462 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER A 58 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A 85 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 292 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 87 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 294 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 89 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 84 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 339 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 86 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA A 341 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 88 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A 338 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 428 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER A 340 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP A 427 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU A 96 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 236 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 231 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A 139 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR A 441 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS A 443 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 344 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER B 58 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER B 85 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA B 292 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 87 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR B 294 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 89 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 84 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE B 339 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 86 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA B 341 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY B 88 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET B 338 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 428 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER B 340 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP B 427 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU B 96 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 231 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 139 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 247 removed outlier: 3.539A pdb=" N THR B 441 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 443 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 344 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER C 58 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER C 85 " --> pdb=" O MET C 290 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 292 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 87 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR C 294 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 89 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 84 " --> pdb=" O TYR C 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 339 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU C 86 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA C 341 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY C 88 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET C 338 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 428 " --> pdb=" O MET C 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 340 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP C 427 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU C 96 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 231 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS C 139 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR C 441 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS C 443 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA C 344 " --> pdb=" O GLN C 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER D 58 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER D 85 " --> pdb=" O MET D 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA D 292 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 87 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR D 294 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 89 " --> pdb=" O TYR D 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE D 84 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 339 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 86 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA D 341 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 88 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET D 338 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU D 428 " --> pdb=" O MET D 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER D 340 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP D 427 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU D 96 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 236 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 231 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS D 139 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR D 441 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS D 443 " --> pdb=" O PRO D 431 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA D 344 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER E 58 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER E 85 " --> pdb=" O MET E 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA E 292 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 87 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR E 294 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA E 89 " --> pdb=" O TYR E 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE E 84 " --> pdb=" O TYR E 337 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE E 339 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU E 86 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA E 341 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY E 88 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET E 338 " --> pdb=" O LEU E 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU E 428 " --> pdb=" O MET E 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER E 340 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP E 427 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU E 96 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU E 236 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 231 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS E 139 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.541A pdb=" N THR E 441 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS E 443 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA E 344 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER F 58 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER F 85 " --> pdb=" O MET F 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA F 292 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 87 " --> pdb=" O ALA F 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR F 294 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA F 89 " --> pdb=" O TYR F 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE F 84 " --> pdb=" O TYR F 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE F 339 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU F 86 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA F 341 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY F 88 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET F 338 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU F 428 " --> pdb=" O MET F 338 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER F 340 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP F 427 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU F 96 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU F 236 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE F 231 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS F 139 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR F 441 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS F 443 " --> pdb=" O PRO F 431 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA F 344 " --> pdb=" O GLN F 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER G 58 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER G 85 " --> pdb=" O MET G 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA G 292 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE G 87 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR G 294 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA G 89 " --> pdb=" O TYR G 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE G 84 " --> pdb=" O TYR G 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE G 339 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU G 86 " --> pdb=" O ILE G 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA G 341 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY G 88 " --> pdb=" O ALA G 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET G 338 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU G 428 " --> pdb=" O MET G 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER G 340 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP G 427 " --> pdb=" O LYS G 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU G 96 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU G 236 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 231 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS G 139 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR G 441 " --> pdb=" O LEU G 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS G 443 " --> pdb=" O PRO G 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA G 344 " --> pdb=" O GLN G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER H 58 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER H 85 " --> pdb=" O MET H 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA H 292 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE H 87 " --> pdb=" O ALA H 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR H 294 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA H 89 " --> pdb=" O TYR H 294 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE H 84 " --> pdb=" O TYR H 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE H 339 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 86 " --> pdb=" O ILE H 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA H 341 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY H 88 " --> pdb=" O ALA H 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET H 338 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU H 428 " --> pdb=" O MET H 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER H 340 " --> pdb=" O LEU H 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP H 427 " --> pdb=" O LYS H 370 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 114 through 117 removed outlier: 4.479A pdb=" N LEU H 96 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU H 236 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE H 231 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS H 139 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR H 441 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS H 443 " --> pdb=" O PRO H 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA H 344 " --> pdb=" O GLN H 432 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER I 58 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER I 85 " --> pdb=" O MET I 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA I 292 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE I 87 " --> pdb=" O ALA I 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR I 294 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA I 89 " --> pdb=" O TYR I 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE I 84 " --> pdb=" O TYR I 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE I 339 " --> pdb=" O PHE I 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU I 86 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA I 341 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY I 88 " --> pdb=" O ALA I 341 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 338 " --> pdb=" O LEU I 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU I 428 " --> pdb=" O MET I 338 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER I 340 " --> pdb=" O LEU I 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP I 427 " --> pdb=" O LYS I 370 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU I 96 " --> pdb=" O LEU I 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU I 236 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE I 231 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS I 139 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR I 441 " --> pdb=" O LEU I 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS I 443 " --> pdb=" O PRO I 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA I 344 " --> pdb=" O GLN I 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER J 58 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER J 85 " --> pdb=" O MET J 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA J 292 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE J 87 " --> pdb=" O ALA J 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR J 294 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA J 89 " --> pdb=" O TYR J 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE J 84 " --> pdb=" O TYR J 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE J 339 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU J 86 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA J 341 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY J 88 " --> pdb=" O ALA J 341 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET J 338 " --> pdb=" O LEU J 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU J 428 " --> pdb=" O MET J 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER J 340 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP J 427 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU J 96 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU J 236 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE J 231 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS J 139 " --> pdb=" O ILE J 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR J 441 " --> pdb=" O LEU J 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS J 443 " --> pdb=" O PRO J 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA J 344 " --> pdb=" O GLN J 432 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER K 58 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER K 85 " --> pdb=" O MET K 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA K 292 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE K 87 " --> pdb=" O ALA K 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR K 294 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA K 89 " --> pdb=" O TYR K 294 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE K 84 " --> pdb=" O TYR K 337 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE K 339 " --> pdb=" O PHE K 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU K 86 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA K 341 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY K 88 " --> pdb=" O ALA K 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET K 338 " --> pdb=" O LEU K 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU K 428 " --> pdb=" O MET K 338 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER K 340 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP K 427 " --> pdb=" O LYS K 370 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU K 96 " --> pdb=" O LEU K 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU K 236 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE K 231 " --> pdb=" O LYS K 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS K 139 " --> pdb=" O ILE K 231 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 245 through 247 removed outlier: 3.541A pdb=" N THR K 441 " --> pdb=" O LEU K 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS K 443 " --> pdb=" O PRO K 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA K 344 " --> pdb=" O GLN K 432 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER L 58 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER L 85 " --> pdb=" O MET L 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA L 292 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE L 87 " --> pdb=" O ALA L 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR L 294 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA L 89 " --> pdb=" O TYR L 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE L 84 " --> pdb=" O TYR L 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE L 339 " --> pdb=" O PHE L 84 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU L 86 " --> pdb=" O ILE L 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA L 341 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY L 88 " --> pdb=" O ALA L 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET L 338 " --> pdb=" O LEU L 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU L 428 " --> pdb=" O MET L 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER L 340 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP L 427 " --> pdb=" O LYS L 370 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU L 96 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU L 236 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE L 231 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS L 139 " --> pdb=" O ILE L 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR L 441 " --> pdb=" O LEU L 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS L 443 " --> pdb=" O PRO L 431 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA L 344 " --> pdb=" O GLN L 432 " (cutoff:3.500A) 1801 hydrogen bonds defined for protein. 4899 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: 16.06 Time building geometry restraints manager: 16.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10587 1.33 - 1.45: 6610 1.45 - 1.57: 22451 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 39948 Sorted by residual: bond pdb=" CA THR L 189 " pdb=" C THR L 189 " ideal model delta sigma weight residual 1.522 1.471 0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" CA THR K 189 " pdb=" C THR K 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR E 189 " pdb=" C THR E 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR B 189 " pdb=" C THR B 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR J 189 " pdb=" C THR J 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.82e+01 ... (remaining 39943 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 1584 106.78 - 113.60: 22581 113.60 - 120.41: 14936 120.41 - 127.23: 14515 127.23 - 134.05: 516 Bond angle restraints: 54132 Sorted by residual: angle pdb=" N LEU J 262 " pdb=" CA LEU J 262 " pdb=" C LEU J 262 " ideal model delta sigma weight residual 113.18 104.73 8.45 1.21e+00 6.83e-01 4.87e+01 angle pdb=" N LEU A 262 " pdb=" CA LEU A 262 " pdb=" C LEU A 262 " ideal model delta sigma weight residual 113.18 104.75 8.43 1.21e+00 6.83e-01 4.85e+01 angle pdb=" N LEU G 262 " pdb=" CA LEU G 262 " pdb=" C LEU G 262 " ideal model delta sigma weight residual 113.18 104.77 8.41 1.21e+00 6.83e-01 4.83e+01 angle pdb=" N LEU F 262 " pdb=" CA LEU F 262 " pdb=" C LEU F 262 " ideal model delta sigma weight residual 113.18 104.77 8.41 1.21e+00 6.83e-01 4.83e+01 angle pdb=" N LEU K 262 " pdb=" CA LEU K 262 " pdb=" C LEU K 262 " ideal model delta sigma weight residual 113.18 104.78 8.40 1.21e+00 6.83e-01 4.82e+01 ... (remaining 54127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 21603 14.52 - 29.04: 1749 29.04 - 43.56: 576 43.56 - 58.07: 252 58.07 - 72.59: 84 Dihedral angle restraints: 24264 sinusoidal: 9636 harmonic: 14628 Sorted by residual: dihedral pdb=" N ASN B 261 " pdb=" C ASN B 261 " pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " ideal model delta harmonic sigma weight residual 122.80 136.34 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N ASN D 261 " pdb=" C ASN D 261 " pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " ideal model delta harmonic sigma weight residual 122.80 136.33 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N ASN L 261 " pdb=" C ASN L 261 " pdb=" CA ASN L 261 " pdb=" CB ASN L 261 " ideal model delta harmonic sigma weight residual 122.80 136.32 -13.52 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 24261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6036 0.131 - 0.263: 162 0.263 - 0.394: 42 0.394 - 0.525: 12 0.525 - 0.656: 12 Chirality restraints: 6264 Sorted by residual: chirality pdb=" CA ASN G 261 " pdb=" N ASN G 261 " pdb=" C ASN G 261 " pdb=" CB ASN G 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASN B 261 " pdb=" N ASN B 261 " pdb=" C ASN B 261 " pdb=" CB ASN B 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASN D 261 " pdb=" N ASN D 261 " pdb=" C ASN D 261 " pdb=" CB ASN D 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 6261 not shown) Planarity restraints: 6972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY G 414 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO G 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO G 415 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 415 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 414 " 0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO E 415 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 415 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 415 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 414 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 415 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.033 5.00e-02 4.00e+02 ... (remaining 6969 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 60 2.12 - 2.81: 11332 2.81 - 3.51: 54905 3.51 - 4.20: 99182 4.20 - 4.90: 175991 Nonbonded interactions: 341470 Sorted by model distance: nonbonded pdb=" OD1 ASP A 342 " pdb="ZN ZN A 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP J 342 " pdb="ZN ZN J 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP D 342 " pdb="ZN ZN D 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP B 342 " pdb="ZN ZN B 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP I 342 " pdb="ZN ZN I 502 " model vdw 1.424 2.230 ... (remaining 341465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 5.730 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 106.670 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.006 0.052 39948 Z= 0.424 Angle : 0.945 8.525 54132 Z= 0.583 Chirality : 0.068 0.656 6264 Planarity : 0.006 0.057 6972 Dihedral : 14.002 72.593 14736 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.32 % Allowed : 7.56 % Favored : 87.11 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 4944 helix: 0.67 (0.13), residues: 1632 sheet: -0.21 (0.15), residues: 1104 loop : -1.12 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 122 HIS 0.009 0.001 HIS D 90 PHE 0.018 0.002 PHE D 461 TYR 0.011 0.001 TYR C 337 ARG 0.004 0.001 ARG C 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1223 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7427 (tptt) REVERT: A 111 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: A 115 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6483 (tm-30) REVERT: A 147 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5807 (pm20) REVERT: A 193 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: A 194 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: A 227 SER cc_start: 0.8206 (m) cc_final: 0.7665 (t) REVERT: A 251 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7305 (mp0) REVERT: A 261 ASN cc_start: 0.6418 (m-40) cc_final: 0.6171 (m-40) REVERT: A 270 GLN cc_start: 0.8009 (tp40) cc_final: 0.7178 (tp40) REVERT: A 274 ASP cc_start: 0.8735 (m-30) cc_final: 0.8284 (m-30) REVERT: A 297 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 326 LEU cc_start: 0.8688 (mp) cc_final: 0.8463 (mt) REVERT: A 372 ASN cc_start: 0.6321 (t0) cc_final: 0.5956 (t0) REVERT: B 19 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7965 (mtmm) REVERT: B 99 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6809 (tptp) REVERT: B 115 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6509 (tm-30) REVERT: B 147 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5432 (pm20) REVERT: B 227 SER cc_start: 0.7902 (m) cc_final: 0.7424 (t) REVERT: B 235 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 251 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7040 (mp0) REVERT: B 261 ASN cc_start: 0.6574 (m-40) cc_final: 0.5540 (m-40) REVERT: B 273 ILE cc_start: 0.8309 (mt) cc_final: 0.8088 (pt) REVERT: B 297 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 318 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7887 (mtp180) REVERT: B 326 LEU cc_start: 0.8303 (mp) cc_final: 0.7969 (mt) REVERT: B 331 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 365 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7518 (mtpp) REVERT: B 371 VAL cc_start: 0.8310 (t) cc_final: 0.8009 (m) REVERT: B 372 ASN cc_start: 0.6201 (t0) cc_final: 0.5835 (t0) REVERT: B 423 LEU cc_start: 0.9073 (tp) cc_final: 0.8729 (tt) REVERT: B 460 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8161 (tp) REVERT: C 19 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8173 (mtmt) REVERT: C 34 CYS cc_start: 0.8268 (m) cc_final: 0.8028 (m) REVERT: C 97 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7660 (mmt-90) REVERT: C 99 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7239 (tptp) REVERT: C 111 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: C 147 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5870 (pm20) REVERT: C 193 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: C 194 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: C 227 SER cc_start: 0.8232 (m) cc_final: 0.7760 (t) REVERT: C 251 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7224 (mp0) REVERT: C 261 ASN cc_start: 0.6773 (m-40) cc_final: 0.6570 (m-40) REVERT: C 290 MET cc_start: 0.8837 (ttp) cc_final: 0.8620 (ttp) REVERT: C 297 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 326 LEU cc_start: 0.7855 (mp) cc_final: 0.7557 (mp) REVERT: C 423 LEU cc_start: 0.9079 (tp) cc_final: 0.8867 (tt) REVERT: D 60 TYR cc_start: 0.7941 (m-80) cc_final: 0.7578 (m-80) REVERT: D 97 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7405 (mmm160) REVERT: D 147 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: D 179 MET cc_start: 0.7358 (tpt) cc_final: 0.6986 (tpt) REVERT: D 251 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7228 (mp0) REVERT: D 270 GLN cc_start: 0.8376 (tp40) cc_final: 0.8011 (tp40) REVERT: D 274 ASP cc_start: 0.8550 (m-30) cc_final: 0.8349 (m-30) REVERT: D 282 LEU cc_start: 0.8639 (tp) cc_final: 0.8393 (tp) REVERT: D 290 MET cc_start: 0.8788 (ttp) cc_final: 0.8379 (ttp) REVERT: D 296 ASN cc_start: 0.8864 (m-40) cc_final: 0.8657 (m-40) REVERT: D 326 LEU cc_start: 0.7984 (mp) cc_final: 0.7712 (mt) REVERT: D 372 ASN cc_start: 0.5891 (t0) cc_final: 0.5689 (t0) REVERT: D 435 MET cc_start: 0.6344 (ttp) cc_final: 0.5897 (ttp) REVERT: D 460 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8103 (tp) REVERT: E 19 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7924 (mtmt) REVERT: E 46 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7177 (mm) REVERT: E 97 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7783 (mmt180) REVERT: E 99 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7390 (tmtt) REVERT: E 132 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8783 (mt) REVERT: E 147 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: E 192 GLN cc_start: 0.8039 (mm110) cc_final: 0.7768 (mm-40) REVERT: E 193 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: E 194 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: E 251 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7300 (mm-30) REVERT: E 297 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7804 (tm-30) REVERT: E 326 LEU cc_start: 0.7747 (mp) cc_final: 0.7467 (mp) REVERT: E 435 MET cc_start: 0.6185 (ttp) cc_final: 0.5596 (ttp) REVERT: F 97 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7800 (mmt180) REVERT: F 147 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5765 (pm20) REVERT: F 179 MET cc_start: 0.7483 (tpt) cc_final: 0.7032 (mmm) REVERT: F 193 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: F 194 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: F 227 SER cc_start: 0.8191 (m) cc_final: 0.7728 (t) REVERT: F 251 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7255 (mp0) REVERT: F 261 ASN cc_start: 0.6443 (m-40) cc_final: 0.5273 (m-40) REVERT: F 265 CYS cc_start: 0.8526 (m) cc_final: 0.8057 (m) REVERT: F 274 ASP cc_start: 0.8684 (m-30) cc_final: 0.8410 (m-30) REVERT: F 297 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7752 (tm-30) REVERT: F 331 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6808 (mt-10) REVERT: F 371 VAL cc_start: 0.8517 (t) cc_final: 0.8261 (m) REVERT: F 372 ASN cc_start: 0.5947 (t0) cc_final: 0.5639 (t0) REVERT: F 460 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8089 (tp) REVERT: G 60 TYR cc_start: 0.8085 (m-80) cc_final: 0.7706 (m-80) REVERT: G 92 ASP cc_start: 0.8367 (p0) cc_final: 0.8090 (p0) REVERT: G 97 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7480 (mmt180) REVERT: G 99 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7389 (tptt) REVERT: G 115 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6601 (tm-30) REVERT: G 147 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5740 (pm20) REVERT: G 193 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: G 194 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: G 237 CYS cc_start: 0.8108 (m) cc_final: 0.7636 (m) REVERT: G 251 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7291 (mp0) REVERT: G 261 ASN cc_start: 0.6711 (m-40) cc_final: 0.6413 (m-40) REVERT: G 270 GLN cc_start: 0.8258 (tp40) cc_final: 0.7556 (tp40) REVERT: G 274 ASP cc_start: 0.8604 (m-30) cc_final: 0.8206 (m-30) REVERT: G 290 MET cc_start: 0.8883 (ttp) cc_final: 0.8613 (ttp) REVERT: G 326 LEU cc_start: 0.7825 (mp) cc_final: 0.7495 (mp) REVERT: G 371 VAL cc_start: 0.8546 (t) cc_final: 0.8284 (m) REVERT: G 372 ASN cc_start: 0.5898 (t0) cc_final: 0.5658 (t0) REVERT: G 389 GLU cc_start: 0.7703 (tp30) cc_final: 0.7240 (tp30) REVERT: G 460 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8147 (tt) REVERT: H 34 CYS cc_start: 0.7999 (m) cc_final: 0.7786 (m) REVERT: H 99 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6889 (tptp) REVERT: H 147 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5949 (pm20) REVERT: H 192 GLN cc_start: 0.8063 (mm110) cc_final: 0.7774 (mm-40) REVERT: H 194 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: H 226 LEU cc_start: 0.7734 (mt) cc_final: 0.7519 (mt) REVERT: H 227 SER cc_start: 0.8239 (m) cc_final: 0.7608 (t) REVERT: H 251 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7191 (mp0) REVERT: H 261 ASN cc_start: 0.6152 (m-40) cc_final: 0.5529 (m-40) REVERT: H 270 GLN cc_start: 0.8218 (tp40) cc_final: 0.7772 (tp40) REVERT: H 297 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7599 (tm-30) REVERT: H 326 LEU cc_start: 0.8534 (mp) cc_final: 0.8243 (mt) REVERT: H 331 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6887 (mt-10) REVERT: H 345 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6758 (p-80) REVERT: H 365 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7714 (mtpp) REVERT: H 372 ASN cc_start: 0.5945 (t0) cc_final: 0.5666 (t0) REVERT: I 46 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (mm) REVERT: I 97 ARG cc_start: 0.8002 (mmt180) cc_final: 0.7499 (mmt-90) REVERT: I 99 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7082 (tptp) REVERT: I 115 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6597 (tm-30) REVERT: I 139 LYS cc_start: 0.6159 (tmtt) cc_final: 0.5954 (tptp) REVERT: I 147 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5318 (pm20) REVERT: I 227 SER cc_start: 0.8186 (m) cc_final: 0.7627 (t) REVERT: I 251 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7248 (mp0) REVERT: I 261 ASN cc_start: 0.6176 (m-40) cc_final: 0.5824 (m-40) REVERT: I 297 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 326 LEU cc_start: 0.8206 (mp) cc_final: 0.7996 (mt) REVERT: I 360 ARG cc_start: 0.5052 (mtp180) cc_final: 0.3513 (ptp-170) REVERT: I 365 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7716 (mtpp) REVERT: I 459 GLU cc_start: 0.7545 (pp20) cc_final: 0.7286 (pp20) REVERT: I 460 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8115 (tp) REVERT: J 34 CYS cc_start: 0.8288 (m) cc_final: 0.7963 (m) REVERT: J 46 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7428 (mm) REVERT: J 60 TYR cc_start: 0.7881 (m-80) cc_final: 0.7409 (m-80) REVERT: J 147 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5819 (pm20) REVERT: J 193 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: J 251 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7195 (mp0) REVERT: J 290 MET cc_start: 0.8904 (ttp) cc_final: 0.8473 (ttp) REVERT: J 297 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7830 (tm-30) REVERT: J 435 MET cc_start: 0.6124 (ttp) cc_final: 0.5877 (ttp) REVERT: K 34 CYS cc_start: 0.8005 (m) cc_final: 0.7758 (m) REVERT: K 46 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7409 (mm) REVERT: K 97 ARG cc_start: 0.8166 (mmt180) cc_final: 0.7876 (mmt180) REVERT: K 99 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7317 (tmtt) REVERT: K 115 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6358 (mt-10) REVERT: K 132 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8689 (mt) REVERT: K 147 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5329 (pm20) REVERT: K 194 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: K 235 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7206 (mt-10) REVERT: K 251 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7197 (mp0) REVERT: K 261 ASN cc_start: 0.6108 (m-40) cc_final: 0.5797 (m-40) REVERT: K 273 ILE cc_start: 0.8309 (mt) cc_final: 0.8099 (pt) REVERT: K 297 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7787 (tm-30) REVERT: K 326 LEU cc_start: 0.8295 (mp) cc_final: 0.7880 (mp) REVERT: L 34 CYS cc_start: 0.8193 (m) cc_final: 0.7986 (m) REVERT: L 46 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7342 (mm) REVERT: L 97 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7730 (mmt180) REVERT: L 147 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: L 179 MET cc_start: 0.7251 (tpt) cc_final: 0.6878 (tpt) REVERT: L 192 GLN cc_start: 0.8114 (mm110) cc_final: 0.7729 (mm-40) REVERT: L 194 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: L 251 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6995 (mp0) REVERT: L 253 PHE cc_start: 0.8722 (m-10) cc_final: 0.8510 (m-10) REVERT: L 270 GLN cc_start: 0.8242 (tp40) cc_final: 0.8015 (tp40) REVERT: L 274 ASP cc_start: 0.8631 (m-30) cc_final: 0.8359 (m-30) REVERT: L 297 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7916 (tm-30) REVERT: L 433 LEU cc_start: 0.8750 (mt) cc_final: 0.8539 (mt) REVERT: L 435 MET cc_start: 0.5918 (ttp) cc_final: 0.5309 (ttp) outliers start: 228 outliers final: 82 residues processed: 1379 average time/residue: 0.5495 time to fit residues: 1205.6121 Evaluate side-chains 1134 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1003 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 111 GLN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.9990 chunk 382 optimal weight: 0.0170 chunk 211 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 457 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 106 GLN A 296 ASN A 432 GLN B 106 GLN B 308 GLN B 348 HIS ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 296 ASN E 65 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 111 GLN J 192 GLN K 11 GLN K 296 ASN K 380 ASN L 82 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39948 Z= 0.168 Angle : 0.579 10.841 54132 Z= 0.297 Chirality : 0.044 0.196 6264 Planarity : 0.005 0.045 6972 Dihedral : 7.978 89.460 5709 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.30 % Allowed : 13.49 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 4944 helix: 1.21 (0.12), residues: 1632 sheet: -0.30 (0.14), residues: 1152 loop : -1.07 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 125 HIS 0.008 0.001 HIS L 90 PHE 0.022 0.002 PHE A 461 TYR 0.008 0.001 TYR J 337 ARG 0.006 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1078 time to evaluate : 4.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7163 (ptt180) cc_final: 0.6957 (ptt180) REVERT: A 33 GLU cc_start: 0.8214 (tp30) cc_final: 0.7987 (tp30) REVERT: A 60 TYR cc_start: 0.7892 (m-80) cc_final: 0.7421 (m-80) REVERT: A 99 LYS cc_start: 0.7988 (tppp) cc_final: 0.7370 (tptt) REVERT: A 115 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6424 (tm-30) REVERT: A 192 GLN cc_start: 0.7874 (mm110) cc_final: 0.6909 (mm110) REVERT: A 219 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7271 (mm) REVERT: A 227 SER cc_start: 0.8099 (m) cc_final: 0.7589 (t) REVERT: A 251 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7084 (mp0) REVERT: A 261 ASN cc_start: 0.6416 (t0) cc_final: 0.5663 (m-40) REVERT: A 297 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 372 ASN cc_start: 0.6237 (t0) cc_final: 0.5868 (t0) REVERT: A 417 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 19 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7786 (mtmm) REVERT: B 99 LYS cc_start: 0.7559 (tppp) cc_final: 0.6703 (tptp) REVERT: B 106 GLN cc_start: 0.7829 (mm110) cc_final: 0.7037 (mm-40) REVERT: B 219 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 251 GLU cc_start: 0.7825 (mm-30) cc_final: 0.6844 (mp0) REVERT: B 261 ASN cc_start: 0.6458 (t0) cc_final: 0.5964 (m-40) REVERT: B 326 LEU cc_start: 0.8313 (mp) cc_final: 0.7960 (mt) REVERT: B 372 ASN cc_start: 0.6085 (t0) cc_final: 0.5740 (t0) REVERT: B 423 LEU cc_start: 0.8959 (tp) cc_final: 0.8687 (tt) REVERT: C 19 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7793 (mtmt) REVERT: C 34 CYS cc_start: 0.8233 (m) cc_final: 0.8033 (m) REVERT: C 97 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7393 (mmt180) REVERT: C 99 LYS cc_start: 0.7951 (tppp) cc_final: 0.7300 (tptp) REVERT: C 192 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7558 (mm-40) REVERT: C 219 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7575 (mm) REVERT: C 227 SER cc_start: 0.8122 (m) cc_final: 0.7659 (t) REVERT: C 251 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7084 (mp0) REVERT: C 261 ASN cc_start: 0.6333 (t0) cc_final: 0.6116 (m-40) REVERT: C 297 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 46 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6998 (mm) REVERT: D 60 TYR cc_start: 0.7761 (m-80) cc_final: 0.7458 (m-80) REVERT: D 179 MET cc_start: 0.7318 (tpt) cc_final: 0.6929 (tpt) REVERT: D 192 GLN cc_start: 0.7864 (mm110) cc_final: 0.7319 (mm-40) REVERT: D 251 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7076 (mp0) REVERT: D 270 GLN cc_start: 0.8280 (tp40) cc_final: 0.7955 (tp40) REVERT: D 282 LEU cc_start: 0.8693 (tp) cc_final: 0.8471 (tp) REVERT: D 326 LEU cc_start: 0.7976 (mp) cc_final: 0.7584 (mp) REVERT: D 331 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6706 (mt-10) REVERT: D 364 HIS cc_start: 0.8115 (m-70) cc_final: 0.7357 (m-70) REVERT: D 372 ASN cc_start: 0.5534 (t0) cc_final: 0.5248 (t0) REVERT: D 440 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6340 (mt-10) REVERT: E 46 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7013 (mm) REVERT: E 97 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7784 (mmt180) REVERT: E 99 LYS cc_start: 0.7844 (tppp) cc_final: 0.7335 (tmtt) REVERT: E 219 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7639 (mm) REVERT: E 251 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7271 (mm-30) REVERT: E 326 LEU cc_start: 0.7937 (mp) cc_final: 0.7562 (mp) REVERT: F 58 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6483 (p) REVERT: F 60 TYR cc_start: 0.7889 (m-80) cc_final: 0.6874 (m-80) REVERT: F 97 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7663 (mmt180) REVERT: F 219 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7156 (mm) REVERT: F 251 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7141 (mp0) REVERT: F 261 ASN cc_start: 0.5930 (t0) cc_final: 0.4665 (m-40) REVERT: F 265 CYS cc_start: 0.8399 (m) cc_final: 0.8049 (m) REVERT: F 274 ASP cc_start: 0.8756 (m-30) cc_final: 0.8382 (m-30) REVERT: F 295 ASP cc_start: 0.8711 (t0) cc_final: 0.8344 (t0) REVERT: F 297 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7786 (tm-30) REVERT: F 331 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6581 (mt-10) REVERT: F 343 MET cc_start: 0.8183 (mmm) cc_final: 0.7970 (mmm) REVERT: F 372 ASN cc_start: 0.5883 (t0) cc_final: 0.5608 (t0) REVERT: F 417 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7909 (mp) REVERT: G 60 TYR cc_start: 0.7911 (m-80) cc_final: 0.7671 (m-80) REVERT: G 99 LYS cc_start: 0.7867 (tppp) cc_final: 0.7173 (tptp) REVERT: G 115 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6522 (tm-30) REVERT: G 219 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7336 (mm) REVERT: G 251 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7074 (mp0) REVERT: G 270 GLN cc_start: 0.8146 (tp40) cc_final: 0.7442 (tp40) REVERT: G 274 ASP cc_start: 0.8634 (m-30) cc_final: 0.8204 (m-30) REVERT: G 290 MET cc_start: 0.8630 (ttp) cc_final: 0.8206 (ttp) REVERT: G 296 ASN cc_start: 0.8893 (m-40) cc_final: 0.8683 (m-40) REVERT: G 371 VAL cc_start: 0.8301 (t) cc_final: 0.8089 (m) REVERT: G 372 ASN cc_start: 0.6030 (t0) cc_final: 0.5798 (t0) REVERT: G 460 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8098 (tt) REVERT: H 7 LYS cc_start: 0.4684 (pttm) cc_final: 0.4399 (tttm) REVERT: H 34 CYS cc_start: 0.8058 (m) cc_final: 0.7813 (m) REVERT: H 60 TYR cc_start: 0.7885 (m-80) cc_final: 0.7429 (m-80) REVERT: H 82 ASN cc_start: 0.8431 (m-40) cc_final: 0.7958 (m-40) REVERT: H 97 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7843 (mmt180) REVERT: H 99 LYS cc_start: 0.7768 (tppp) cc_final: 0.6870 (tptp) REVERT: H 192 GLN cc_start: 0.7832 (mm110) cc_final: 0.7455 (mm-40) REVERT: H 227 SER cc_start: 0.7994 (m) cc_final: 0.7452 (t) REVERT: H 234 MET cc_start: 0.7091 (mtt) cc_final: 0.6846 (mtt) REVERT: H 251 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7072 (mp0) REVERT: H 297 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7572 (tm-30) REVERT: H 326 LEU cc_start: 0.8532 (mp) cc_final: 0.8209 (mt) REVERT: I 46 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7150 (mm) REVERT: I 139 LYS cc_start: 0.6180 (tmtt) cc_final: 0.5971 (tptp) REVERT: I 251 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7190 (mp0) REVERT: I 261 ASN cc_start: 0.6858 (t0) cc_final: 0.6490 (m-40) REVERT: I 297 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7847 (tm-30) REVERT: I 326 LEU cc_start: 0.8222 (mp) cc_final: 0.7933 (mt) REVERT: I 331 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6807 (mt-10) REVERT: I 400 ASP cc_start: 0.8180 (m-30) cc_final: 0.7771 (m-30) REVERT: I 460 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8075 (tp) REVERT: J 23 ARG cc_start: 0.7123 (ptt180) cc_final: 0.6392 (ptt180) REVERT: J 46 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7273 (mm) REVERT: J 60 TYR cc_start: 0.7744 (m-80) cc_final: 0.7470 (m-80) REVERT: J 99 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7417 (tptp) REVERT: J 251 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7017 (mp0) REVERT: J 261 ASN cc_start: 0.6207 (t0) cc_final: 0.5319 (t0) REVERT: J 265 CYS cc_start: 0.8403 (m) cc_final: 0.8137 (m) REVERT: J 290 MET cc_start: 0.8614 (ttp) cc_final: 0.8380 (ttp) REVERT: J 297 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7859 (tm-30) REVERT: K 34 CYS cc_start: 0.8095 (m) cc_final: 0.7843 (m) REVERT: K 46 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7242 (mm) REVERT: K 99 LYS cc_start: 0.8021 (tppp) cc_final: 0.7344 (tptp) REVERT: K 115 GLU cc_start: 0.6468 (tm-30) cc_final: 0.6190 (mt-10) REVERT: K 189 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7080 (t) REVERT: K 193 GLU cc_start: 0.7730 (pt0) cc_final: 0.7200 (pt0) REVERT: K 235 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7160 (mt-10) REVERT: K 251 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7127 (mp0) REVERT: K 297 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7980 (tm-30) REVERT: K 384 GLU cc_start: 0.7532 (tp30) cc_final: 0.7328 (tp30) REVERT: K 388 ARG cc_start: 0.6548 (mtp85) cc_final: 0.6247 (mtp180) REVERT: L 34 CYS cc_start: 0.8191 (m) cc_final: 0.7909 (m) REVERT: L 46 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7292 (mm) REVERT: L 60 TYR cc_start: 0.7694 (m-80) cc_final: 0.7038 (m-80) REVERT: L 179 MET cc_start: 0.7385 (tpt) cc_final: 0.7106 (tpt) REVERT: L 192 GLN cc_start: 0.7836 (mm110) cc_final: 0.7633 (mm-40) REVERT: L 219 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7465 (mm) REVERT: L 251 GLU cc_start: 0.7754 (mm-30) cc_final: 0.6995 (mp0) REVERT: L 253 PHE cc_start: 0.8682 (m-80) cc_final: 0.8439 (m-10) REVERT: L 297 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7941 (tm-30) outliers start: 184 outliers final: 95 residues processed: 1199 average time/residue: 0.5217 time to fit residues: 1023.0744 Evaluate side-chains 1066 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 952 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 380 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 458 optimal weight: 3.9990 chunk 495 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 454 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 367 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 148 GLN A 192 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 296 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN H 65 ASN H 106 GLN H 296 ASN I 223 HIS ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 148 GLN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 148 GLN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 39948 Z= 0.356 Angle : 0.661 9.532 54132 Z= 0.336 Chirality : 0.047 0.240 6264 Planarity : 0.005 0.040 6972 Dihedral : 5.918 54.383 5507 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.58 % Allowed : 15.71 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 4944 helix: 1.03 (0.13), residues: 1632 sheet: -0.22 (0.15), residues: 1104 loop : -1.28 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 122 HIS 0.009 0.002 HIS E 90 PHE 0.019 0.002 PHE H 461 TYR 0.012 0.002 TYR H 337 ARG 0.007 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 963 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7160 (ptt180) cc_final: 0.6677 (ptt180) REVERT: A 115 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6512 (tm-30) REVERT: A 192 GLN cc_start: 0.7888 (mm-40) cc_final: 0.6872 (mm110) REVERT: A 219 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 227 SER cc_start: 0.8059 (m) cc_final: 0.7520 (t) REVERT: A 251 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7154 (mp0) REVERT: A 261 ASN cc_start: 0.6297 (t0) cc_final: 0.5658 (m-40) REVERT: A 297 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 343 MET cc_start: 0.8124 (mmm) cc_final: 0.7805 (mmt) REVERT: A 372 ASN cc_start: 0.6325 (t0) cc_final: 0.5921 (t0) REVERT: A 384 GLU cc_start: 0.7248 (tp30) cc_final: 0.7036 (tp30) REVERT: A 417 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 440 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6038 (tt0) REVERT: B 19 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8024 (mtmm) REVERT: B 99 LYS cc_start: 0.7655 (tppp) cc_final: 0.6771 (tptp) REVERT: B 192 GLN cc_start: 0.7649 (mm110) cc_final: 0.7429 (mm-40) REVERT: B 219 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7060 (mm) REVERT: B 227 SER cc_start: 0.7893 (m) cc_final: 0.7343 (t) REVERT: B 235 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: B 251 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7042 (mp0) REVERT: B 261 ASN cc_start: 0.6428 (t0) cc_final: 0.5523 (m-40) REVERT: B 326 LEU cc_start: 0.8370 (mp) cc_final: 0.8014 (mt) REVERT: B 360 ARG cc_start: 0.4839 (mtp180) cc_final: 0.3659 (ptp-170) REVERT: B 372 ASN cc_start: 0.6272 (t0) cc_final: 0.5838 (t0) REVERT: C 97 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7587 (mmt180) REVERT: C 99 LYS cc_start: 0.7998 (tppp) cc_final: 0.7264 (tptp) REVERT: C 192 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7704 (mm-40) REVERT: C 227 SER cc_start: 0.8116 (m) cc_final: 0.7632 (t) REVERT: C 251 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7111 (mp0) REVERT: C 261 ASN cc_start: 0.6100 (t0) cc_final: 0.5830 (m-40) REVERT: C 274 ASP cc_start: 0.8725 (m-30) cc_final: 0.8416 (m-30) REVERT: C 290 MET cc_start: 0.8648 (ttp) cc_final: 0.8370 (ttp) REVERT: C 297 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 7 LYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3849 (pttm) REVERT: D 60 TYR cc_start: 0.7984 (m-80) cc_final: 0.7639 (m-80) REVERT: D 97 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7719 (mmt180) REVERT: D 179 MET cc_start: 0.7288 (tpt) cc_final: 0.6808 (tpt) REVERT: D 192 GLN cc_start: 0.7918 (mm110) cc_final: 0.7291 (mm-40) REVERT: D 234 MET cc_start: 0.6300 (mmm) cc_final: 0.5995 (mmt) REVERT: D 251 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7138 (mp0) REVERT: D 261 ASN cc_start: 0.6412 (t0) cc_final: 0.6129 (t0) REVERT: D 270 GLN cc_start: 0.8394 (tp40) cc_final: 0.8168 (tp40) REVERT: D 282 LEU cc_start: 0.8694 (tp) cc_final: 0.8473 (tp) REVERT: D 326 LEU cc_start: 0.8296 (mp) cc_final: 0.8086 (mt) REVERT: D 331 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6697 (mt-10) REVERT: D 360 ARG cc_start: 0.4942 (mtp180) cc_final: 0.3216 (ptp-170) REVERT: D 372 ASN cc_start: 0.5917 (t0) cc_final: 0.5665 (t0) REVERT: E 46 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7148 (mm) REVERT: E 97 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7782 (mmt180) REVERT: E 99 LYS cc_start: 0.7932 (tppp) cc_final: 0.7344 (tptp) REVERT: E 129 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: E 192 GLN cc_start: 0.7952 (mm110) cc_final: 0.7478 (mm-40) REVERT: E 219 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7591 (mm) REVERT: E 251 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7697 (mm-30) REVERT: E 295 ASP cc_start: 0.8818 (t0) cc_final: 0.8540 (t0) REVERT: E 326 LEU cc_start: 0.8124 (mp) cc_final: 0.7777 (mp) REVERT: F 97 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7801 (mmt180) REVERT: F 219 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7234 (mm) REVERT: F 234 MET cc_start: 0.6798 (mmt) cc_final: 0.6261 (mmt) REVERT: F 251 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7143 (mp0) REVERT: F 274 ASP cc_start: 0.8832 (m-30) cc_final: 0.8437 (m-30) REVERT: F 295 ASP cc_start: 0.8756 (t0) cc_final: 0.8454 (t0) REVERT: F 297 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7833 (tm-30) REVERT: F 331 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6695 (mt-10) REVERT: F 372 ASN cc_start: 0.6131 (t0) cc_final: 0.5885 (t0) REVERT: F 417 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8023 (mp) REVERT: G 60 TYR cc_start: 0.8205 (m-80) cc_final: 0.7850 (m-80) REVERT: G 92 ASP cc_start: 0.8291 (p0) cc_final: 0.8021 (p0) REVERT: G 115 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6592 (tm-30) REVERT: G 193 GLU cc_start: 0.7528 (pt0) cc_final: 0.7299 (pt0) REVERT: G 219 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7267 (mm) REVERT: G 251 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7056 (mp0) REVERT: G 274 ASP cc_start: 0.8674 (m-30) cc_final: 0.8100 (m-30) REVERT: G 290 MET cc_start: 0.8699 (ttp) cc_final: 0.8482 (ttp) REVERT: G 296 ASN cc_start: 0.9053 (m110) cc_final: 0.8772 (m-40) REVERT: G 371 VAL cc_start: 0.8553 (t) cc_final: 0.8306 (m) REVERT: G 372 ASN cc_start: 0.6234 (t0) cc_final: 0.5979 (t0) REVERT: G 388 ARG cc_start: 0.6754 (mtm180) cc_final: 0.6312 (mtm180) REVERT: G 432 GLN cc_start: 0.8713 (tt0) cc_final: 0.8507 (tt0) REVERT: G 460 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8240 (tt) REVERT: H 23 ARG cc_start: 0.7240 (ptt180) cc_final: 0.6429 (ptt180) REVERT: H 34 CYS cc_start: 0.8043 (m) cc_final: 0.7825 (m) REVERT: H 60 TYR cc_start: 0.8138 (m-80) cc_final: 0.7455 (m-80) REVERT: H 97 ARG cc_start: 0.8162 (mmt180) cc_final: 0.7919 (mmt180) REVERT: H 99 LYS cc_start: 0.7822 (tppp) cc_final: 0.6941 (tptp) REVERT: H 192 GLN cc_start: 0.7852 (mm110) cc_final: 0.7376 (mm-40) REVERT: H 227 SER cc_start: 0.8081 (m) cc_final: 0.7493 (t) REVERT: H 234 MET cc_start: 0.7207 (mtt) cc_final: 0.6954 (mtt) REVERT: H 251 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7283 (mp0) REVERT: H 261 ASN cc_start: 0.6200 (m-40) cc_final: 0.5827 (m-40) REVERT: H 296 ASN cc_start: 0.8937 (m110) cc_final: 0.8471 (m110) REVERT: H 297 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7556 (tm-30) REVERT: H 326 LEU cc_start: 0.8486 (mp) cc_final: 0.8137 (mt) REVERT: I 7 LYS cc_start: 0.4008 (OUTLIER) cc_final: 0.3364 (pttm) REVERT: I 46 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7177 (mm) REVERT: I 139 LYS cc_start: 0.6115 (tmtt) cc_final: 0.5710 (tptp) REVERT: I 232 LEU cc_start: 0.8256 (mp) cc_final: 0.7970 (mp) REVERT: I 251 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7191 (mp0) REVERT: I 261 ASN cc_start: 0.6474 (t0) cc_final: 0.6143 (m-40) REVERT: I 297 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7840 (tm-30) REVERT: I 326 LEU cc_start: 0.8251 (mp) cc_final: 0.7965 (mt) REVERT: I 331 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6691 (mt-10) REVERT: I 360 ARG cc_start: 0.4973 (mtp180) cc_final: 0.3573 (ptp-170) REVERT: I 386 LEU cc_start: 0.8341 (mm) cc_final: 0.8120 (mp) REVERT: J 21 VAL cc_start: 0.9153 (m) cc_final: 0.8943 (t) REVERT: J 23 ARG cc_start: 0.7088 (ptt180) cc_final: 0.6414 (ptt180) REVERT: J 46 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7340 (mm) REVERT: J 60 TYR cc_start: 0.7989 (m-80) cc_final: 0.7515 (m-80) REVERT: J 97 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7725 (mmt180) REVERT: J 251 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7042 (mp0) REVERT: J 261 ASN cc_start: 0.6497 (t0) cc_final: 0.5770 (t0) REVERT: J 265 CYS cc_start: 0.8399 (m) cc_final: 0.8165 (m) REVERT: J 290 MET cc_start: 0.8817 (ttp) cc_final: 0.8327 (ttp) REVERT: J 297 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8026 (tm-30) REVERT: K 34 CYS cc_start: 0.8222 (m) cc_final: 0.7935 (m) REVERT: K 46 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7366 (mm) REVERT: K 99 LYS cc_start: 0.8026 (tppp) cc_final: 0.7208 (tptp) REVERT: K 115 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6301 (mt-10) REVERT: K 193 GLU cc_start: 0.7761 (pt0) cc_final: 0.7427 (pt0) REVERT: K 232 LEU cc_start: 0.8653 (mp) cc_final: 0.8281 (mp) REVERT: K 235 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7079 (mt-10) REVERT: K 251 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7088 (mp0) REVERT: K 297 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7809 (tm-30) REVERT: K 384 GLU cc_start: 0.7633 (tp30) cc_final: 0.7411 (tp30) REVERT: L 34 CYS cc_start: 0.8189 (m) cc_final: 0.7937 (m) REVERT: L 40 GLN cc_start: 0.8046 (mp10) cc_final: 0.7843 (mp10) REVERT: L 46 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7394 (mm) REVERT: L 60 TYR cc_start: 0.8037 (m-80) cc_final: 0.7063 (m-80) REVERT: L 115 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6297 (tm-30) REVERT: L 179 MET cc_start: 0.7263 (tpt) cc_final: 0.6975 (tpt) REVERT: L 192 GLN cc_start: 0.7989 (mm110) cc_final: 0.7676 (mm-40) REVERT: L 219 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7437 (mm) REVERT: L 232 LEU cc_start: 0.8178 (mp) cc_final: 0.7888 (mp) REVERT: L 234 MET cc_start: 0.6960 (mmt) cc_final: 0.6723 (mmt) REVERT: L 251 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7001 (mp0) REVERT: L 297 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7926 (tm-30) REVERT: L 384 GLU cc_start: 0.7514 (tp30) cc_final: 0.7301 (tp30) outliers start: 196 outliers final: 143 residues processed: 1075 average time/residue: 0.5269 time to fit residues: 921.3209 Evaluate side-chains 1068 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 907 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 309 SER Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 309 SER Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 1.9990 chunk 344 optimal weight: 0.0980 chunk 237 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 487 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 436 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 overall best weight: 1.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 192 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 152 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 296 ASN ** L 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39948 Z= 0.247 Angle : 0.595 12.064 54132 Z= 0.303 Chirality : 0.045 0.219 6264 Planarity : 0.004 0.037 6972 Dihedral : 5.510 52.987 5497 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.55 % Allowed : 17.41 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 4944 helix: 1.01 (0.12), residues: 1632 sheet: -0.28 (0.15), residues: 1104 loop : -1.25 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 122 HIS 0.008 0.001 HIS K 90 PHE 0.015 0.002 PHE I 461 TYR 0.011 0.001 TYR E 60 ARG 0.007 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 955 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6668 (ptt180) REVERT: A 99 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7280 (tptp) REVERT: A 115 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6476 (tm-30) REVERT: A 192 GLN cc_start: 0.7877 (mm110) cc_final: 0.6839 (mm110) REVERT: A 219 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 227 SER cc_start: 0.8028 (m) cc_final: 0.7511 (t) REVERT: A 251 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7134 (mp0) REVERT: A 261 ASN cc_start: 0.6234 (t0) cc_final: 0.5835 (m-40) REVERT: A 297 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 372 ASN cc_start: 0.6288 (t0) cc_final: 0.5907 (t0) REVERT: A 417 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 7 LYS cc_start: 0.4036 (OUTLIER) cc_final: 0.3621 (pttm) REVERT: B 99 LYS cc_start: 0.7575 (tppp) cc_final: 0.6684 (tptp) REVERT: B 192 GLN cc_start: 0.7693 (mm110) cc_final: 0.7433 (mm-40) REVERT: B 219 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6903 (mm) REVERT: B 227 SER cc_start: 0.7895 (m) cc_final: 0.7360 (t) REVERT: B 251 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7033 (mp0) REVERT: B 261 ASN cc_start: 0.6371 (t0) cc_final: 0.6151 (m-40) REVERT: B 289 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7124 (mtt180) REVERT: B 326 LEU cc_start: 0.8409 (mp) cc_final: 0.8060 (mt) REVERT: B 360 ARG cc_start: 0.4820 (mtp180) cc_final: 0.3137 (mtt-85) REVERT: B 372 ASN cc_start: 0.6205 (t0) cc_final: 0.5818 (t0) REVERT: B 398 LEU cc_start: 0.8906 (mp) cc_final: 0.8600 (mp) REVERT: B 440 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5738 (tt0) REVERT: C 192 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7589 (mm-40) REVERT: C 227 SER cc_start: 0.8081 (m) cc_final: 0.7623 (t) REVERT: C 251 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7102 (mp0) REVERT: C 261 ASN cc_start: 0.6585 (t0) cc_final: 0.6181 (m-40) REVERT: C 274 ASP cc_start: 0.8736 (m-30) cc_final: 0.8419 (m-30) REVERT: C 290 MET cc_start: 0.8578 (ttp) cc_final: 0.8307 (ttp) REVERT: C 297 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7693 (tm-30) REVERT: D 179 MET cc_start: 0.7239 (tpt) cc_final: 0.6825 (tpt) REVERT: D 192 GLN cc_start: 0.7889 (mm110) cc_final: 0.7224 (mm-40) REVERT: D 251 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7134 (mp0) REVERT: D 326 LEU cc_start: 0.8289 (mp) cc_final: 0.8030 (mt) REVERT: D 331 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6653 (mt-10) REVERT: D 360 ARG cc_start: 0.4919 (mtp180) cc_final: 0.2925 (mtt-85) REVERT: D 372 ASN cc_start: 0.5814 (t0) cc_final: 0.5572 (t0) REVERT: E 15 ARG cc_start: 0.6654 (mtt-85) cc_final: 0.6287 (mmt180) REVERT: E 46 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6974 (mm) REVERT: E 99 LYS cc_start: 0.7918 (tppp) cc_final: 0.7301 (tptp) REVERT: E 193 GLU cc_start: 0.7642 (tt0) cc_final: 0.7310 (pt0) REVERT: E 219 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7462 (mm) REVERT: E 235 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6998 (mt-10) REVERT: E 251 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 326 LEU cc_start: 0.8239 (mp) cc_final: 0.7982 (mt) REVERT: F 7 LYS cc_start: 0.4194 (OUTLIER) cc_final: 0.3829 (pttm) REVERT: F 60 TYR cc_start: 0.7950 (m-80) cc_final: 0.7214 (m-80) REVERT: F 97 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7773 (mmt180) REVERT: F 219 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7308 (mm) REVERT: F 251 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7121 (mp0) REVERT: F 261 ASN cc_start: 0.6055 (t0) cc_final: 0.5657 (m-40) REVERT: F 274 ASP cc_start: 0.8771 (m-30) cc_final: 0.8374 (m-30) REVERT: F 295 ASP cc_start: 0.8797 (t0) cc_final: 0.8450 (t0) REVERT: F 297 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7716 (tm-30) REVERT: F 331 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6653 (mt-10) REVERT: F 417 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7978 (mp) REVERT: F 427 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (t0) REVERT: G 7 LYS cc_start: 0.4912 (OUTLIER) cc_final: 0.4481 (pttm) REVERT: G 60 TYR cc_start: 0.8081 (m-80) cc_final: 0.7674 (m-80) REVERT: G 92 ASP cc_start: 0.8167 (p0) cc_final: 0.7947 (p0) REVERT: G 115 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6454 (tm-30) REVERT: G 192 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7388 (mm110) REVERT: G 193 GLU cc_start: 0.7467 (pt0) cc_final: 0.7177 (pt0) REVERT: G 219 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7398 (mm) REVERT: G 251 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7029 (mp0) REVERT: G 274 ASP cc_start: 0.8662 (m-30) cc_final: 0.8122 (m-30) REVERT: G 296 ASN cc_start: 0.9007 (m110) cc_final: 0.8703 (m-40) REVERT: G 371 VAL cc_start: 0.8533 (t) cc_final: 0.8282 (m) REVERT: G 372 ASN cc_start: 0.6087 (t0) cc_final: 0.5856 (t0) REVERT: G 388 ARG cc_start: 0.6631 (mtm180) cc_final: 0.6046 (mtm180) REVERT: G 460 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8174 (tt) REVERT: H 23 ARG cc_start: 0.7246 (ptt180) cc_final: 0.6398 (ptt180) REVERT: H 34 CYS cc_start: 0.8043 (m) cc_final: 0.7817 (m) REVERT: H 60 TYR cc_start: 0.8013 (m-80) cc_final: 0.7431 (m-80) REVERT: H 82 ASN cc_start: 0.8453 (m-40) cc_final: 0.8036 (m-40) REVERT: H 97 ARG cc_start: 0.8106 (mmt180) cc_final: 0.7880 (mmt180) REVERT: H 139 LYS cc_start: 0.5476 (tptp) cc_final: 0.5255 (tptp) REVERT: H 192 GLN cc_start: 0.7774 (mm110) cc_final: 0.7079 (mm110) REVERT: H 227 SER cc_start: 0.8055 (m) cc_final: 0.7466 (t) REVERT: H 234 MET cc_start: 0.7182 (mtt) cc_final: 0.6962 (mtt) REVERT: H 251 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7289 (mp0) REVERT: H 289 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6980 (mtt180) REVERT: H 297 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7505 (tm-30) REVERT: H 326 LEU cc_start: 0.8465 (mp) cc_final: 0.8114 (mt) REVERT: I 46 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7153 (mm) REVERT: I 139 LYS cc_start: 0.6089 (tmtt) cc_final: 0.5686 (tptp) REVERT: I 232 LEU cc_start: 0.8367 (mp) cc_final: 0.8076 (mp) REVERT: I 251 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7161 (mp0) REVERT: I 261 ASN cc_start: 0.6576 (t0) cc_final: 0.6216 (m-40) REVERT: I 297 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7789 (tm-30) REVERT: I 326 LEU cc_start: 0.8291 (mp) cc_final: 0.8007 (mt) REVERT: I 331 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6599 (mt-10) REVERT: I 343 MET cc_start: 0.8477 (mmm) cc_final: 0.8111 (mmm) REVERT: I 360 ARG cc_start: 0.4779 (mtp180) cc_final: 0.3053 (mtt90) REVERT: J 23 ARG cc_start: 0.7080 (ptt180) cc_final: 0.6505 (ptt180) REVERT: J 46 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7318 (mm) REVERT: J 60 TYR cc_start: 0.7934 (m-80) cc_final: 0.7470 (m-80) REVERT: J 97 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7623 (mmt180) REVERT: J 192 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7436 (mm110) REVERT: J 193 GLU cc_start: 0.7462 (pt0) cc_final: 0.7251 (pt0) REVERT: J 235 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7231 (mt-10) REVERT: J 251 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7047 (mp0) REVERT: J 261 ASN cc_start: 0.6244 (t0) cc_final: 0.5304 (t0) REVERT: J 265 CYS cc_start: 0.8351 (m) cc_final: 0.8102 (m) REVERT: J 290 MET cc_start: 0.8727 (ttp) cc_final: 0.8314 (ttp) REVERT: J 297 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7919 (tm-30) REVERT: K 21 VAL cc_start: 0.9257 (m) cc_final: 0.9041 (t) REVERT: K 34 CYS cc_start: 0.8196 (m) cc_final: 0.7961 (m) REVERT: K 46 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7272 (mm) REVERT: K 99 LYS cc_start: 0.7990 (tppp) cc_final: 0.7264 (tptp) REVERT: K 115 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6399 (mt-10) REVERT: K 193 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: K 251 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7126 (mp0) REVERT: K 290 MET cc_start: 0.8694 (ttp) cc_final: 0.8456 (ttm) REVERT: K 297 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7615 (tm-30) REVERT: K 384 GLU cc_start: 0.7618 (tp30) cc_final: 0.7380 (tp30) REVERT: L 34 CYS cc_start: 0.8205 (m) cc_final: 0.7948 (m) REVERT: L 46 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7354 (mm) REVERT: L 60 TYR cc_start: 0.7905 (m-80) cc_final: 0.7082 (m-80) REVERT: L 115 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6138 (tm-30) REVERT: L 147 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5697 (pt0) REVERT: L 192 GLN cc_start: 0.8001 (mm110) cc_final: 0.7648 (mm-40) REVERT: L 219 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7343 (mm) REVERT: L 232 LEU cc_start: 0.8165 (mp) cc_final: 0.7893 (mp) REVERT: L 234 MET cc_start: 0.6973 (mmt) cc_final: 0.6443 (mmt) REVERT: L 251 GLU cc_start: 0.7811 (mm-30) cc_final: 0.6969 (mp0) REVERT: L 297 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7875 (tm-30) REVERT: L 384 GLU cc_start: 0.7510 (tp30) cc_final: 0.7264 (tp30) outliers start: 195 outliers final: 133 residues processed: 1071 average time/residue: 0.5642 time to fit residues: 994.4482 Evaluate side-chains 1073 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 918 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 GLU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 400 ASP Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 415 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 437 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 192 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 152 HIS H 106 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN K 296 ASN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39948 Z= 0.246 Angle : 0.591 9.995 54132 Z= 0.300 Chirality : 0.045 0.212 6264 Planarity : 0.004 0.037 6972 Dihedral : 5.344 52.471 5489 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.00 % Allowed : 18.23 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 4944 helix: 0.86 (0.12), residues: 1704 sheet: -0.33 (0.15), residues: 1104 loop : -1.25 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 122 HIS 0.009 0.001 HIS B 364 PHE 0.015 0.002 PHE I 461 TYR 0.010 0.001 TYR H 337 ARG 0.007 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 943 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.3508 (pttm) REVERT: A 55 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7270 (mmtm) REVERT: A 60 TYR cc_start: 0.8031 (m-80) cc_final: 0.7426 (m-80) REVERT: A 99 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7009 (tptp) REVERT: A 115 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6485 (tm-30) REVERT: A 129 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: A 192 GLN cc_start: 0.7847 (mm-40) cc_final: 0.6793 (mm110) REVERT: A 219 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7133 (mm) REVERT: A 227 SER cc_start: 0.8204 (m) cc_final: 0.7668 (t) REVERT: A 234 MET cc_start: 0.7193 (mmt) cc_final: 0.6455 (mmt) REVERT: A 251 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7145 (mp0) REVERT: A 261 ASN cc_start: 0.6284 (t0) cc_final: 0.5961 (m-40) REVERT: A 289 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7385 (mtt180) REVERT: A 297 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 372 ASN cc_start: 0.6185 (t0) cc_final: 0.5792 (t0) REVERT: A 384 GLU cc_start: 0.7292 (tp30) cc_final: 0.7024 (tp30) REVERT: A 417 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 7 LYS cc_start: 0.4063 (OUTLIER) cc_final: 0.3627 (pttm) REVERT: B 99 LYS cc_start: 0.7618 (tppp) cc_final: 0.6754 (tptp) REVERT: B 181 MET cc_start: 0.8126 (ptt) cc_final: 0.7397 (tmm) REVERT: B 192 GLN cc_start: 0.7673 (mm110) cc_final: 0.7160 (mm-40) REVERT: B 227 SER cc_start: 0.7874 (m) cc_final: 0.7362 (t) REVERT: B 234 MET cc_start: 0.7030 (mmt) cc_final: 0.6553 (mmt) REVERT: B 251 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7037 (mp0) REVERT: B 261 ASN cc_start: 0.6405 (t0) cc_final: 0.6175 (m-40) REVERT: B 289 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7172 (mtt180) REVERT: B 326 LEU cc_start: 0.8402 (mp) cc_final: 0.8060 (mt) REVERT: B 348 HIS cc_start: 0.8468 (t-90) cc_final: 0.8235 (t-170) REVERT: B 360 ARG cc_start: 0.4817 (mtp180) cc_final: 0.3169 (mtt-85) REVERT: B 372 ASN cc_start: 0.6337 (t0) cc_final: 0.5972 (t0) REVERT: B 427 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7442 (t0) REVERT: B 440 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5709 (tt0) REVERT: C 192 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7541 (mm-40) REVERT: C 193 GLU cc_start: 0.6955 (pt0) cc_final: 0.6666 (pt0) REVERT: C 219 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7622 (mm) REVERT: C 227 SER cc_start: 0.8064 (m) cc_final: 0.7605 (t) REVERT: C 235 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7307 (mt-10) REVERT: C 251 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7110 (mp0) REVERT: C 261 ASN cc_start: 0.6406 (t0) cc_final: 0.6060 (m-40) REVERT: C 274 ASP cc_start: 0.8718 (m-30) cc_final: 0.8394 (m-30) REVERT: C 290 MET cc_start: 0.8626 (ttp) cc_final: 0.8367 (ttp) REVERT: C 297 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 179 MET cc_start: 0.7191 (tpt) cc_final: 0.6801 (tpt) REVERT: D 192 GLN cc_start: 0.7907 (mm110) cc_final: 0.7302 (mm-40) REVERT: D 251 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 289 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: D 326 LEU cc_start: 0.8269 (mp) cc_final: 0.8037 (mt) REVERT: D 331 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6688 (mt-10) REVERT: D 360 ARG cc_start: 0.4723 (mtp180) cc_final: 0.2899 (mtt-85) REVERT: D 372 ASN cc_start: 0.5774 (t0) cc_final: 0.5528 (t0) REVERT: E 7 LYS cc_start: 0.4771 (OUTLIER) cc_final: 0.4451 (pttm) REVERT: E 46 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7010 (mm) REVERT: E 99 LYS cc_start: 0.7907 (tppp) cc_final: 0.7276 (tptp) REVERT: E 192 GLN cc_start: 0.7978 (mm110) cc_final: 0.7776 (mm110) REVERT: E 193 GLU cc_start: 0.7592 (tt0) cc_final: 0.7192 (pt0) REVERT: E 251 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7142 (mm-30) REVERT: E 297 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 326 LEU cc_start: 0.8297 (mp) cc_final: 0.8049 (mt) REVERT: E 384 GLU cc_start: 0.7583 (tp30) cc_final: 0.7319 (tp30) REVERT: E 398 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8684 (mp) REVERT: F 7 LYS cc_start: 0.4204 (OUTLIER) cc_final: 0.3954 (pttm) REVERT: F 60 TYR cc_start: 0.7965 (m-80) cc_final: 0.7179 (m-80) REVERT: F 97 ARG cc_start: 0.8046 (mmt180) cc_final: 0.7752 (mmt180) REVERT: F 147 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5065 (pm20) REVERT: F 234 MET cc_start: 0.7257 (mmt) cc_final: 0.7015 (mmt) REVERT: F 251 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7128 (mp0) REVERT: F 295 ASP cc_start: 0.8793 (t0) cc_final: 0.8477 (t0) REVERT: F 297 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7720 (tm-30) REVERT: F 331 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6628 (mt-10) REVERT: F 417 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (mp) REVERT: F 427 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7864 (t0) REVERT: G 7 LYS cc_start: 0.4939 (OUTLIER) cc_final: 0.4470 (pttm) REVERT: G 60 TYR cc_start: 0.8077 (m-80) cc_final: 0.7730 (m-80) REVERT: G 92 ASP cc_start: 0.8199 (p0) cc_final: 0.7960 (p0) REVERT: G 115 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6480 (tm-30) REVERT: G 192 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7366 (mm110) REVERT: G 193 GLU cc_start: 0.7315 (pt0) cc_final: 0.7066 (pt0) REVERT: G 251 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7046 (mp0) REVERT: G 261 ASN cc_start: 0.6610 (m-40) cc_final: 0.6376 (m-40) REVERT: G 274 ASP cc_start: 0.8753 (m-30) cc_final: 0.8150 (m-30) REVERT: G 296 ASN cc_start: 0.8979 (m110) cc_final: 0.8679 (m-40) REVERT: G 371 VAL cc_start: 0.8497 (t) cc_final: 0.8241 (m) REVERT: G 372 ASN cc_start: 0.6153 (t0) cc_final: 0.5927 (t0) REVERT: H 23 ARG cc_start: 0.7201 (ptt180) cc_final: 0.6334 (ptt180) REVERT: H 34 CYS cc_start: 0.8025 (m) cc_final: 0.7800 (m) REVERT: H 60 TYR cc_start: 0.7999 (m-80) cc_final: 0.7400 (m-80) REVERT: H 82 ASN cc_start: 0.8500 (m-40) cc_final: 0.8089 (m-40) REVERT: H 97 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7873 (mmt180) REVERT: H 99 LYS cc_start: 0.7910 (ttmm) cc_final: 0.6953 (tptp) REVERT: H 192 GLN cc_start: 0.7863 (mm110) cc_final: 0.7629 (mm-40) REVERT: H 227 SER cc_start: 0.8038 (m) cc_final: 0.7490 (t) REVERT: H 251 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7256 (mp0) REVERT: H 297 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7703 (tm-30) REVERT: H 326 LEU cc_start: 0.8499 (mp) cc_final: 0.8128 (mt) REVERT: H 427 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7417 (t0) REVERT: H 440 GLU cc_start: 0.6358 (mt-10) cc_final: 0.6103 (mt-10) REVERT: I 7 LYS cc_start: 0.3980 (OUTLIER) cc_final: 0.3610 (pttm) REVERT: I 139 LYS cc_start: 0.6081 (tmtt) cc_final: 0.5744 (tptp) REVERT: I 232 LEU cc_start: 0.8287 (mp) cc_final: 0.7985 (mp) REVERT: I 234 MET cc_start: 0.7106 (mmt) cc_final: 0.6628 (mmt) REVERT: I 251 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7162 (mp0) REVERT: I 261 ASN cc_start: 0.6624 (t0) cc_final: 0.6286 (m-40) REVERT: I 297 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7734 (tm-30) REVERT: I 326 LEU cc_start: 0.8389 (mp) cc_final: 0.8112 (mt) REVERT: I 331 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6560 (mt-10) REVERT: I 343 MET cc_start: 0.8519 (mmm) cc_final: 0.8108 (mmm) REVERT: I 360 ARG cc_start: 0.4844 (mtp180) cc_final: 0.3098 (mtt90) REVERT: J 23 ARG cc_start: 0.7157 (ptt180) cc_final: 0.6593 (ptt180) REVERT: J 46 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7285 (mm) REVERT: J 60 TYR cc_start: 0.7924 (m-80) cc_final: 0.7515 (m-80) REVERT: J 129 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: J 155 ARG cc_start: 0.8456 (ptt-90) cc_final: 0.8206 (ptt-90) REVERT: J 192 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7436 (mm110) REVERT: J 193 GLU cc_start: 0.7193 (pt0) cc_final: 0.6955 (pt0) REVERT: J 235 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7117 (mt-10) REVERT: J 251 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7086 (mp0) REVERT: J 261 ASN cc_start: 0.6203 (t0) cc_final: 0.5388 (t0) REVERT: J 265 CYS cc_start: 0.8317 (m) cc_final: 0.8073 (m) REVERT: J 290 MET cc_start: 0.8711 (ttp) cc_final: 0.8325 (ttp) REVERT: J 297 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7884 (tm-30) REVERT: J 386 LEU cc_start: 0.8646 (mm) cc_final: 0.8446 (mp) REVERT: K 21 VAL cc_start: 0.9270 (m) cc_final: 0.9065 (t) REVERT: K 34 CYS cc_start: 0.8174 (m) cc_final: 0.7959 (m) REVERT: K 97 ARG cc_start: 0.8226 (mmt180) cc_final: 0.8015 (mmt180) REVERT: K 99 LYS cc_start: 0.7997 (tppp) cc_final: 0.7324 (tptp) REVERT: K 115 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6378 (mt-10) REVERT: K 251 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7118 (mp0) REVERT: K 297 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7525 (tm-30) REVERT: K 384 GLU cc_start: 0.7613 (tp30) cc_final: 0.7369 (tp30) REVERT: L 34 CYS cc_start: 0.8208 (m) cc_final: 0.7951 (m) REVERT: L 46 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7260 (mm) REVERT: L 60 TYR cc_start: 0.7885 (m-80) cc_final: 0.7137 (m-80) REVERT: L 97 ARG cc_start: 0.7954 (mmt180) cc_final: 0.7696 (mmt180) REVERT: L 115 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6202 (tm-30) REVERT: L 192 GLN cc_start: 0.8058 (mm110) cc_final: 0.7706 (mm-40) REVERT: L 219 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7288 (mm) REVERT: L 232 LEU cc_start: 0.8185 (mp) cc_final: 0.7920 (mp) REVERT: L 251 GLU cc_start: 0.7776 (mm-30) cc_final: 0.6972 (mp0) REVERT: L 297 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 214 outliers final: 150 residues processed: 1066 average time/residue: 0.5243 time to fit residues: 902.5285 Evaluate side-chains 1075 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 901 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 400 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 309 SER Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 400 ASP Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 286 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 487 optimal weight: 5.9990 chunk 404 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN C 29 HIS C 65 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 308 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 HIS ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 152 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39948 Z= 0.170 Angle : 0.556 13.639 54132 Z= 0.281 Chirality : 0.044 0.190 6264 Planarity : 0.004 0.036 6972 Dihedral : 4.962 53.544 5483 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.65 % Allowed : 19.19 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 4944 helix: 1.11 (0.12), residues: 1632 sheet: -0.35 (0.15), residues: 1104 loop : -1.20 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 122 HIS 0.006 0.001 HIS B 364 PHE 0.021 0.001 PHE L 461 TYR 0.011 0.001 TYR E 60 ARG 0.007 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 966 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7010 (ptt180) cc_final: 0.6535 (ptt180) REVERT: A 55 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7320 (mmtm) REVERT: A 60 TYR cc_start: 0.7963 (m-80) cc_final: 0.7390 (m-80) REVERT: A 99 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7174 (tptp) REVERT: A 115 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6451 (tm-30) REVERT: A 189 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.6959 (t) REVERT: A 192 GLN cc_start: 0.7829 (mm-40) cc_final: 0.6613 (mm110) REVERT: A 219 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7097 (mm) REVERT: A 227 SER cc_start: 0.8180 (m) cc_final: 0.7693 (t) REVERT: A 234 MET cc_start: 0.7103 (mmt) cc_final: 0.6574 (mmt) REVERT: A 251 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7166 (mp0) REVERT: A 261 ASN cc_start: 0.6384 (t0) cc_final: 0.6050 (m-40) REVERT: A 289 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8114 (mtt180) REVERT: A 297 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 372 ASN cc_start: 0.6078 (t0) cc_final: 0.5684 (t0) REVERT: A 417 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 7 LYS cc_start: 0.4041 (OUTLIER) cc_final: 0.3535 (pttm) REVERT: B 99 LYS cc_start: 0.7649 (tppp) cc_final: 0.7393 (mmmt) REVERT: B 181 MET cc_start: 0.8110 (ptt) cc_final: 0.7376 (tmm) REVERT: B 189 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7331 (t) REVERT: B 192 GLN cc_start: 0.7655 (mm110) cc_final: 0.7137 (mm-40) REVERT: B 219 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6934 (mm) REVERT: B 227 SER cc_start: 0.7861 (m) cc_final: 0.7378 (t) REVERT: B 234 MET cc_start: 0.6898 (mmt) cc_final: 0.6617 (mmt) REVERT: B 251 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7043 (mp0) REVERT: B 261 ASN cc_start: 0.6494 (t0) cc_final: 0.6258 (m-40) REVERT: B 326 LEU cc_start: 0.8414 (mp) cc_final: 0.8071 (mt) REVERT: B 339 ILE cc_start: 0.9126 (mt) cc_final: 0.8921 (mt) REVERT: B 348 HIS cc_start: 0.8470 (t-90) cc_final: 0.8266 (t-170) REVERT: B 360 ARG cc_start: 0.4832 (mtp180) cc_final: 0.3169 (mtt-85) REVERT: B 372 ASN cc_start: 0.6078 (t0) cc_final: 0.5828 (t0) REVERT: B 427 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 192 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7526 (mm-40) REVERT: C 219 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7648 (mm) REVERT: C 227 SER cc_start: 0.7985 (m) cc_final: 0.7489 (t) REVERT: C 251 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7131 (mp0) REVERT: C 261 ASN cc_start: 0.6527 (t0) cc_final: 0.6126 (m-40) REVERT: C 270 GLN cc_start: 0.8204 (tp40) cc_final: 0.7687 (tp40) REVERT: C 274 ASP cc_start: 0.8648 (m-30) cc_final: 0.8332 (m-30) REVERT: C 290 MET cc_start: 0.8556 (ttp) cc_final: 0.8303 (ttp) REVERT: C 297 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 60 TYR cc_start: 0.7791 (m-80) cc_final: 0.7267 (m-80) REVERT: D 97 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7424 (mmm-85) REVERT: D 127 ASP cc_start: 0.8735 (m-30) cc_final: 0.8333 (m-30) REVERT: D 179 MET cc_start: 0.7132 (tpt) cc_final: 0.6781 (tpt) REVERT: D 181 MET cc_start: 0.8185 (ptt) cc_final: 0.7441 (tmm) REVERT: D 192 GLN cc_start: 0.7879 (mm110) cc_final: 0.7272 (mm-40) REVERT: D 193 GLU cc_start: 0.6969 (pt0) cc_final: 0.6733 (pt0) REVERT: D 289 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7728 (mtt180) REVERT: D 326 LEU cc_start: 0.8306 (mp) cc_final: 0.8031 (mt) REVERT: D 331 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6694 (mt-10) REVERT: D 360 ARG cc_start: 0.5029 (mtp180) cc_final: 0.3165 (mtt-85) REVERT: E 7 LYS cc_start: 0.4673 (OUTLIER) cc_final: 0.4273 (pttm) REVERT: E 21 VAL cc_start: 0.9179 (m) cc_final: 0.8954 (t) REVERT: E 46 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6927 (mm) REVERT: E 99 LYS cc_start: 0.8005 (tppp) cc_final: 0.7627 (mmmt) REVERT: E 193 GLU cc_start: 0.7450 (tt0) cc_final: 0.7115 (pt0) REVERT: E 219 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7570 (mm) REVERT: E 251 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7490 (mm-30) REVERT: E 297 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 326 LEU cc_start: 0.8281 (mp) cc_final: 0.8039 (mt) REVERT: E 460 LEU cc_start: 0.8519 (tp) cc_final: 0.8288 (tt) REVERT: F 7 LYS cc_start: 0.4134 (OUTLIER) cc_final: 0.3658 (pttm) REVERT: F 15 ARG cc_start: 0.6644 (mtt-85) cc_final: 0.6284 (mmt180) REVERT: F 19 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8090 (mtmm) REVERT: F 60 TYR cc_start: 0.7872 (m-80) cc_final: 0.7216 (m-80) REVERT: F 92 ASP cc_start: 0.7787 (p0) cc_final: 0.7525 (p0) REVERT: F 234 MET cc_start: 0.7452 (mmt) cc_final: 0.6903 (mmt) REVERT: F 251 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7527 (mm-30) REVERT: F 289 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7240 (mtt180) REVERT: F 297 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7769 (tm-30) REVERT: F 331 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6662 (mt-10) REVERT: F 417 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7984 (mp) REVERT: F 427 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7809 (t0) REVERT: G 6 ARG cc_start: 0.6137 (mtm-85) cc_final: 0.5469 (ptp90) REVERT: G 7 LYS cc_start: 0.4910 (OUTLIER) cc_final: 0.4073 (pttm) REVERT: G 21 VAL cc_start: 0.9204 (m) cc_final: 0.8970 (t) REVERT: G 60 TYR cc_start: 0.8046 (m-80) cc_final: 0.7680 (m-80) REVERT: G 192 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7343 (mm-40) REVERT: G 219 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7206 (mm) REVERT: G 251 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7043 (mp0) REVERT: G 261 ASN cc_start: 0.6509 (m-40) cc_final: 0.6307 (m-40) REVERT: G 274 ASP cc_start: 0.8738 (m-30) cc_final: 0.8532 (m-30) REVERT: G 360 ARG cc_start: 0.4385 (mtp180) cc_final: 0.3150 (mtt90) REVERT: G 371 VAL cc_start: 0.8506 (t) cc_final: 0.8264 (m) REVERT: H 60 TYR cc_start: 0.7897 (m-80) cc_final: 0.7402 (m-80) REVERT: H 82 ASN cc_start: 0.8614 (m-40) cc_final: 0.8094 (m-40) REVERT: H 99 LYS cc_start: 0.7852 (ttmm) cc_final: 0.6830 (tptp) REVERT: H 192 GLN cc_start: 0.7821 (mm110) cc_final: 0.7580 (mm-40) REVERT: H 227 SER cc_start: 0.8019 (m) cc_final: 0.7482 (t) REVERT: H 251 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7253 (mp0) REVERT: H 289 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7697 (mtt180) REVERT: H 297 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7475 (tm-30) REVERT: H 326 LEU cc_start: 0.8448 (mp) cc_final: 0.8166 (mt) REVERT: H 427 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7392 (t0) REVERT: I 7 LYS cc_start: 0.3896 (OUTLIER) cc_final: 0.3444 (pttm) REVERT: I 47 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7594 (mmmt) REVERT: I 227 SER cc_start: 0.8118 (m) cc_final: 0.7490 (t) REVERT: I 232 LEU cc_start: 0.8300 (mp) cc_final: 0.7943 (mp) REVERT: I 234 MET cc_start: 0.6852 (mmt) cc_final: 0.6405 (mmt) REVERT: I 235 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7012 (mt-10) REVERT: I 251 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7159 (mp0) REVERT: I 261 ASN cc_start: 0.6502 (t0) cc_final: 0.6204 (m-40) REVERT: I 289 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7727 (mtt180) REVERT: I 297 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7723 (tm-30) REVERT: I 326 LEU cc_start: 0.8392 (mp) cc_final: 0.8144 (mt) REVERT: I 331 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6544 (mt-10) REVERT: I 360 ARG cc_start: 0.4717 (mtp180) cc_final: 0.3085 (mtt90) REVERT: I 386 LEU cc_start: 0.8406 (mm) cc_final: 0.8189 (mp) REVERT: J 23 ARG cc_start: 0.7092 (ptt180) cc_final: 0.6570 (ptt180) REVERT: J 60 TYR cc_start: 0.7862 (m-80) cc_final: 0.7425 (m-80) REVERT: J 97 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7660 (mmt180) REVERT: J 155 ARG cc_start: 0.8442 (ptt-90) cc_final: 0.8086 (ptt90) REVERT: J 192 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7691 (mm110) REVERT: J 235 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7127 (mt-10) REVERT: J 251 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7074 (mp0) REVERT: J 261 ASN cc_start: 0.6268 (t0) cc_final: 0.5345 (t0) REVERT: J 290 MET cc_start: 0.8582 (ttp) cc_final: 0.8362 (ttp) REVERT: J 297 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7848 (tm-30) REVERT: K 21 VAL cc_start: 0.9263 (m) cc_final: 0.9037 (t) REVERT: K 97 ARG cc_start: 0.8216 (mmt180) cc_final: 0.7979 (mmt180) REVERT: K 99 LYS cc_start: 0.7828 (tppp) cc_final: 0.7100 (tptp) REVERT: K 115 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6253 (mt-10) REVERT: K 251 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7133 (mp0) REVERT: K 289 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7791 (mtt180) REVERT: K 290 MET cc_start: 0.8608 (ttp) cc_final: 0.8397 (ttp) REVERT: K 296 ASN cc_start: 0.8925 (m-40) cc_final: 0.8717 (m-40) REVERT: K 297 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7588 (tm-30) REVERT: K 384 GLU cc_start: 0.7493 (tp30) cc_final: 0.7252 (tp30) REVERT: L 15 ARG cc_start: 0.7169 (mtt-85) cc_final: 0.6766 (mmt180) REVERT: L 34 CYS cc_start: 0.8197 (m) cc_final: 0.7991 (m) REVERT: L 46 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7173 (mm) REVERT: L 60 TYR cc_start: 0.7826 (m-80) cc_final: 0.7201 (m-80) REVERT: L 97 ARG cc_start: 0.7908 (mmt180) cc_final: 0.7692 (mmt180) REVERT: L 192 GLN cc_start: 0.8022 (mm110) cc_final: 0.6935 (mm110) REVERT: L 219 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7227 (mm) REVERT: L 227 SER cc_start: 0.8247 (m) cc_final: 0.7610 (t) REVERT: L 232 LEU cc_start: 0.8078 (mp) cc_final: 0.7769 (mp) REVERT: L 251 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6930 (mp0) REVERT: L 297 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7580 (tm-30) outliers start: 199 outliers final: 132 residues processed: 1099 average time/residue: 0.5327 time to fit residues: 948.4473 Evaluate side-chains 1067 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 909 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 296 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 106 GLN F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 HIS ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39948 Z= 0.278 Angle : 0.617 12.218 54132 Z= 0.309 Chirality : 0.045 0.222 6264 Planarity : 0.004 0.040 6972 Dihedral : 4.964 46.473 5475 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.25 % Allowed : 19.49 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 4944 helix: 0.90 (0.12), residues: 1704 sheet: -0.54 (0.14), residues: 1212 loop : -1.14 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 52 HIS 0.008 0.001 HIS H 90 PHE 0.017 0.002 PHE L 461 TYR 0.011 0.002 TYR E 60 ARG 0.008 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 907 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.4150 (OUTLIER) cc_final: 0.3523 (pttm) REVERT: A 23 ARG cc_start: 0.7108 (ptt180) cc_final: 0.6581 (ptt180) REVERT: A 55 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7660 (mtmm) REVERT: A 60 TYR cc_start: 0.8020 (m-80) cc_final: 0.7331 (m-80) REVERT: A 99 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7186 (tptp) REVERT: A 115 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 192 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7580 (mm110) REVERT: A 219 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7202 (mm) REVERT: A 227 SER cc_start: 0.8215 (m) cc_final: 0.7705 (t) REVERT: A 234 MET cc_start: 0.7261 (mmt) cc_final: 0.7029 (mmt) REVERT: A 250 TYR cc_start: 0.8016 (m-10) cc_final: 0.7529 (m-80) REVERT: A 251 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7208 (mp0) REVERT: A 289 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7368 (mtt180) REVERT: A 297 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 372 ASN cc_start: 0.6176 (t0) cc_final: 0.5751 (t0) REVERT: A 384 GLU cc_start: 0.7335 (tp30) cc_final: 0.7096 (tp30) REVERT: A 417 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 7 LYS cc_start: 0.4145 (OUTLIER) cc_final: 0.3797 (pttm) REVERT: B 99 LYS cc_start: 0.7642 (tppp) cc_final: 0.7378 (mmmt) REVERT: B 181 MET cc_start: 0.8119 (ptt) cc_final: 0.7369 (tmm) REVERT: B 189 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7262 (t) REVERT: B 192 GLN cc_start: 0.7637 (mm110) cc_final: 0.7128 (mm-40) REVERT: B 219 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6941 (mm) REVERT: B 227 SER cc_start: 0.7869 (m) cc_final: 0.7359 (t) REVERT: B 234 MET cc_start: 0.6934 (mmt) cc_final: 0.6546 (mmt) REVERT: B 251 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6990 (mp0) REVERT: B 261 ASN cc_start: 0.6437 (t0) cc_final: 0.6190 (m-40) REVERT: B 274 ASP cc_start: 0.8530 (m-30) cc_final: 0.8271 (m-30) REVERT: B 289 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7266 (mtt180) REVERT: B 326 LEU cc_start: 0.8445 (mp) cc_final: 0.8124 (mt) REVERT: B 348 HIS cc_start: 0.8417 (t-90) cc_final: 0.8185 (t-170) REVERT: B 360 ARG cc_start: 0.4714 (mtp180) cc_final: 0.3533 (mtt90) REVERT: B 398 LEU cc_start: 0.8883 (mp) cc_final: 0.8523 (mp) REVERT: B 427 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7418 (t0) REVERT: C 192 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7598 (mm-40) REVERT: C 219 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7701 (mm) REVERT: C 227 SER cc_start: 0.8042 (m) cc_final: 0.7594 (t) REVERT: C 251 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7047 (mp0) REVERT: C 261 ASN cc_start: 0.6237 (t0) cc_final: 0.5888 (m-40) REVERT: C 274 ASP cc_start: 0.8685 (m-30) cc_final: 0.8349 (m-30) REVERT: C 290 MET cc_start: 0.8697 (ttp) cc_final: 0.8406 (ttp) REVERT: C 297 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 97 ARG cc_start: 0.7898 (mmt180) cc_final: 0.7390 (mmm-85) REVERT: D 179 MET cc_start: 0.7176 (tpt) cc_final: 0.6819 (tpt) REVERT: D 181 MET cc_start: 0.8230 (ptt) cc_final: 0.7436 (tmm) REVERT: D 192 GLN cc_start: 0.7899 (mm110) cc_final: 0.7256 (mm-40) REVERT: D 289 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7759 (mtt180) REVERT: D 326 LEU cc_start: 0.8368 (mp) cc_final: 0.8080 (mt) REVERT: D 331 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6687 (mt-10) REVERT: D 360 ARG cc_start: 0.4873 (mtp180) cc_final: 0.3056 (mtt-85) REVERT: D 365 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7428 (mtpp) REVERT: E 21 VAL cc_start: 0.9243 (m) cc_final: 0.9020 (t) REVERT: E 193 GLU cc_start: 0.7491 (tt0) cc_final: 0.7279 (tt0) REVERT: E 219 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7719 (mm) REVERT: E 251 GLU cc_start: 0.7829 (mm-30) cc_final: 0.6990 (mm-30) REVERT: E 261 ASN cc_start: 0.6680 (m-40) cc_final: 0.6421 (m-40) REVERT: E 297 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 326 LEU cc_start: 0.8315 (mp) cc_final: 0.8094 (mt) REVERT: E 384 GLU cc_start: 0.7559 (tp30) cc_final: 0.7331 (tp30) REVERT: E 460 LEU cc_start: 0.8561 (tp) cc_final: 0.8360 (tt) REVERT: F 60 TYR cc_start: 0.7949 (m-80) cc_final: 0.7224 (m-80) REVERT: F 106 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: F 227 SER cc_start: 0.8070 (m) cc_final: 0.7612 (t) REVERT: F 251 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7157 (mp0) REVERT: F 289 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7206 (mtt180) REVERT: F 295 ASP cc_start: 0.8797 (t0) cc_final: 0.8502 (t0) REVERT: F 297 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7727 (tm-30) REVERT: F 331 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6722 (mt-10) REVERT: F 427 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (t0) REVERT: G 6 ARG cc_start: 0.6071 (mtm-85) cc_final: 0.5515 (ptp90) REVERT: G 7 LYS cc_start: 0.4997 (OUTLIER) cc_final: 0.4369 (pttm) REVERT: G 21 VAL cc_start: 0.9196 (m) cc_final: 0.8961 (t) REVERT: G 60 TYR cc_start: 0.8085 (m-80) cc_final: 0.7717 (m-80) REVERT: G 147 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5487 (pm20) REVERT: G 192 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7421 (mm-40) REVERT: G 219 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7087 (mm) REVERT: G 251 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7147 (mp0) REVERT: G 261 ASN cc_start: 0.6582 (m-40) cc_final: 0.6365 (m-40) REVERT: G 274 ASP cc_start: 0.8737 (m-30) cc_final: 0.8124 (m-30) REVERT: G 289 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7919 (mtt180) REVERT: H 60 TYR cc_start: 0.7922 (m-80) cc_final: 0.7348 (m-80) REVERT: H 82 ASN cc_start: 0.8551 (m-40) cc_final: 0.8102 (m-40) REVERT: H 99 LYS cc_start: 0.7877 (ttmm) cc_final: 0.6955 (tptp) REVERT: H 227 SER cc_start: 0.8041 (m) cc_final: 0.7519 (t) REVERT: H 251 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7273 (mp0) REVERT: H 289 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6976 (mtt180) REVERT: H 297 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7610 (tm-30) REVERT: H 326 LEU cc_start: 0.8464 (mp) cc_final: 0.8187 (mt) REVERT: H 427 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7410 (t0) REVERT: I 46 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7173 (mm) REVERT: I 227 SER cc_start: 0.8124 (m) cc_final: 0.7478 (t) REVERT: I 232 LEU cc_start: 0.8125 (mp) cc_final: 0.7859 (mp) REVERT: I 234 MET cc_start: 0.6975 (mmt) cc_final: 0.6453 (mmt) REVERT: I 251 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7143 (mp0) REVERT: I 261 ASN cc_start: 0.6501 (t0) cc_final: 0.6180 (m-40) REVERT: I 289 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7715 (mtt180) REVERT: I 297 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7760 (tm-30) REVERT: I 326 LEU cc_start: 0.8375 (mp) cc_final: 0.8129 (mt) REVERT: I 331 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6585 (mt-10) REVERT: I 360 ARG cc_start: 0.4715 (mtp180) cc_final: 0.3072 (mtt90) REVERT: J 23 ARG cc_start: 0.7113 (ptt180) cc_final: 0.6566 (ptt180) REVERT: J 46 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7237 (mm) REVERT: J 60 TYR cc_start: 0.7877 (m-80) cc_final: 0.7496 (m-80) REVERT: J 97 ARG cc_start: 0.7942 (mmt180) cc_final: 0.7650 (mmt180) REVERT: J 155 ARG cc_start: 0.8442 (ptt-90) cc_final: 0.8069 (ptt90) REVERT: J 192 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7695 (mm110) REVERT: J 251 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7118 (mp0) REVERT: J 261 ASN cc_start: 0.6148 (t0) cc_final: 0.5614 (t0) REVERT: J 290 MET cc_start: 0.8699 (ttp) cc_final: 0.8406 (ttp) REVERT: J 297 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7918 (tm-30) REVERT: K 21 VAL cc_start: 0.9257 (m) cc_final: 0.9043 (t) REVERT: K 97 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7949 (mmt180) REVERT: K 99 LYS cc_start: 0.7898 (tppp) cc_final: 0.7150 (tptp) REVERT: K 115 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6343 (mt-10) REVERT: K 251 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7173 (mp0) REVERT: K 289 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: K 297 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7692 (tm-30) REVERT: L 15 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6690 (mmt180) REVERT: L 34 CYS cc_start: 0.8199 (m) cc_final: 0.7953 (m) REVERT: L 46 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7212 (mm) REVERT: L 60 TYR cc_start: 0.7863 (m-80) cc_final: 0.7129 (m-80) REVERT: L 87 ILE cc_start: 0.8762 (mt) cc_final: 0.8476 (mp) REVERT: L 97 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7737 (mmt180) REVERT: L 147 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5681 (pt0) REVERT: L 227 SER cc_start: 0.8385 (m) cc_final: 0.7772 (t) REVERT: L 251 GLU cc_start: 0.7770 (mm-30) cc_final: 0.6971 (mp0) REVERT: L 297 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7647 (tm-30) outliers start: 225 outliers final: 160 residues processed: 1041 average time/residue: 0.5709 time to fit residues: 973.5747 Evaluate side-chains 1068 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 881 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 381 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 152 HIS A 296 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 106 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 296 ASN ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39948 Z= 0.230 Angle : 0.605 11.736 54132 Z= 0.303 Chirality : 0.045 0.307 6264 Planarity : 0.004 0.040 6972 Dihedral : 4.864 45.862 5473 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.88 % Allowed : 19.89 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 4944 helix: 1.01 (0.12), residues: 1632 sheet: -0.56 (0.14), residues: 1212 loop : -1.17 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 52 HIS 0.009 0.001 HIS A 90 PHE 0.026 0.002 PHE L 461 TYR 0.011 0.001 TYR E 60 ARG 0.008 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 910 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.4172 (OUTLIER) cc_final: 0.3532 (pttm) REVERT: A 55 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7634 (mtmm) REVERT: A 60 TYR cc_start: 0.7980 (m-80) cc_final: 0.7305 (m-80) REVERT: A 99 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7183 (tptp) REVERT: A 106 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 115 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6517 (tm-30) REVERT: A 129 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: A 192 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7595 (mm110) REVERT: A 219 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7218 (mm) REVERT: A 227 SER cc_start: 0.8206 (m) cc_final: 0.7713 (t) REVERT: A 234 MET cc_start: 0.7181 (mmt) cc_final: 0.6952 (mmt) REVERT: A 250 TYR cc_start: 0.7985 (m-10) cc_final: 0.7507 (m-80) REVERT: A 251 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7131 (mp0) REVERT: A 289 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7836 (mtt180) REVERT: A 297 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 343 MET cc_start: 0.7990 (mmm) cc_final: 0.7786 (mmt) REVERT: A 372 ASN cc_start: 0.6050 (t0) cc_final: 0.5670 (t0) REVERT: A 388 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6439 (mtm180) REVERT: A 417 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 7 LYS cc_start: 0.4128 (OUTLIER) cc_final: 0.3764 (pttm) REVERT: B 99 LYS cc_start: 0.7711 (tppp) cc_final: 0.7460 (mmmt) REVERT: B 189 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7162 (t) REVERT: B 192 GLN cc_start: 0.7553 (mm110) cc_final: 0.6941 (mm-40) REVERT: B 219 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6947 (mm) REVERT: B 227 SER cc_start: 0.7866 (m) cc_final: 0.7363 (t) REVERT: B 234 MET cc_start: 0.6855 (mmt) cc_final: 0.6499 (mmt) REVERT: B 251 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7022 (mp0) REVERT: B 261 ASN cc_start: 0.6440 (t0) cc_final: 0.6174 (m-40) REVERT: B 274 ASP cc_start: 0.8519 (m-30) cc_final: 0.8242 (m-30) REVERT: B 289 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7192 (mtt180) REVERT: B 326 LEU cc_start: 0.8402 (mp) cc_final: 0.8077 (mt) REVERT: B 348 HIS cc_start: 0.8441 (t-90) cc_final: 0.8205 (t-170) REVERT: B 360 ARG cc_start: 0.4734 (mtp180) cc_final: 0.3579 (mtt90) REVERT: B 398 LEU cc_start: 0.8750 (mp) cc_final: 0.8416 (mp) REVERT: B 427 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7403 (t0) REVERT: C 147 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5489 (pm20) REVERT: C 192 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7510 (mm-40) REVERT: C 219 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7700 (mm) REVERT: C 227 SER cc_start: 0.8073 (m) cc_final: 0.7619 (t) REVERT: C 251 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7046 (mp0) REVERT: C 261 ASN cc_start: 0.6236 (t0) cc_final: 0.5863 (m-40) REVERT: C 274 ASP cc_start: 0.8642 (m-30) cc_final: 0.8303 (m-30) REVERT: C 289 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8041 (mtt180) REVERT: C 290 MET cc_start: 0.8618 (ttp) cc_final: 0.8363 (ttp) REVERT: C 297 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 384 GLU cc_start: 0.7331 (tp30) cc_final: 0.7115 (tp30) REVERT: D 97 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7389 (mmm-85) REVERT: D 127 ASP cc_start: 0.8742 (m-30) cc_final: 0.8355 (m-30) REVERT: D 179 MET cc_start: 0.7147 (tpt) cc_final: 0.6770 (tpt) REVERT: D 181 MET cc_start: 0.8267 (ptt) cc_final: 0.7439 (tmm) REVERT: D 192 GLN cc_start: 0.7841 (mm110) cc_final: 0.7255 (mm-40) REVERT: D 235 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7026 (mt-10) REVERT: D 289 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7752 (mtt180) REVERT: D 326 LEU cc_start: 0.8350 (mp) cc_final: 0.8066 (mt) REVERT: D 331 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6708 (mt-10) REVERT: D 343 MET cc_start: 0.8281 (mmm) cc_final: 0.8013 (mmm) REVERT: D 360 ARG cc_start: 0.4949 (mtp180) cc_final: 0.3160 (mtt-85) REVERT: E 7 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4495 (pttm) REVERT: E 21 VAL cc_start: 0.9230 (m) cc_final: 0.8999 (t) REVERT: E 147 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5961 (pt0) REVERT: E 219 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7759 (mm) REVERT: E 235 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 251 GLU cc_start: 0.7824 (mm-30) cc_final: 0.6957 (mm-30) REVERT: E 261 ASN cc_start: 0.6644 (m-40) cc_final: 0.6361 (m-40) REVERT: E 326 LEU cc_start: 0.8282 (mp) cc_final: 0.8076 (mt) REVERT: E 440 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6203 (tt0) REVERT: E 460 LEU cc_start: 0.8580 (tp) cc_final: 0.8367 (tt) REVERT: F 60 TYR cc_start: 0.7911 (m-80) cc_final: 0.7199 (m-80) REVERT: F 106 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: F 227 SER cc_start: 0.8055 (m) cc_final: 0.7611 (t) REVERT: F 234 MET cc_start: 0.7103 (mmt) cc_final: 0.6649 (mmt) REVERT: F 251 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7165 (mp0) REVERT: F 289 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7207 (mtt180) REVERT: F 295 ASP cc_start: 0.8779 (t0) cc_final: 0.8464 (t0) REVERT: F 297 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7723 (tm-30) REVERT: F 331 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6704 (mt-10) REVERT: F 427 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7849 (t0) REVERT: G 6 ARG cc_start: 0.6065 (mtm-85) cc_final: 0.5450 (ptp90) REVERT: G 7 LYS cc_start: 0.4937 (OUTLIER) cc_final: 0.4236 (pttm) REVERT: G 21 VAL cc_start: 0.9188 (m) cc_final: 0.8963 (t) REVERT: G 60 TYR cc_start: 0.8030 (m-80) cc_final: 0.7666 (m-80) REVERT: G 192 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7098 (mm-40) REVERT: G 219 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7091 (mm) REVERT: G 251 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7058 (mp0) REVERT: G 261 ASN cc_start: 0.6407 (m-40) cc_final: 0.6203 (m-40) REVERT: G 274 ASP cc_start: 0.8740 (m-30) cc_final: 0.8112 (m-30) REVERT: G 371 VAL cc_start: 0.8495 (t) cc_final: 0.8234 (m) REVERT: G 372 ASN cc_start: 0.5903 (t0) cc_final: 0.5662 (t0) REVERT: G 384 GLU cc_start: 0.7512 (tp30) cc_final: 0.7299 (tp30) REVERT: H 60 TYR cc_start: 0.7927 (m-80) cc_final: 0.7367 (m-80) REVERT: H 82 ASN cc_start: 0.8607 (m-40) cc_final: 0.8112 (m-40) REVERT: H 99 LYS cc_start: 0.7831 (ttmm) cc_final: 0.6914 (tptp) REVERT: H 192 GLN cc_start: 0.7862 (mm110) cc_final: 0.7582 (mm-40) REVERT: H 227 SER cc_start: 0.8035 (m) cc_final: 0.7516 (t) REVERT: H 251 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7257 (mp0) REVERT: H 252 GLU cc_start: 0.7822 (tt0) cc_final: 0.7410 (tt0) REVERT: H 261 ASN cc_start: 0.6329 (m-40) cc_final: 0.5730 (m-40) REVERT: H 289 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6995 (mtt180) REVERT: H 297 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7447 (tm-30) REVERT: H 326 LEU cc_start: 0.8451 (mp) cc_final: 0.8171 (mt) REVERT: H 343 MET cc_start: 0.8300 (mmm) cc_final: 0.8094 (mmm) REVERT: H 427 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7384 (t0) REVERT: I 6 ARG cc_start: 0.5759 (mtm-85) cc_final: 0.5192 (ptp90) REVERT: I 7 LYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4316 (pttm) REVERT: I 46 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7140 (mm) REVERT: I 227 SER cc_start: 0.8127 (m) cc_final: 0.7484 (t) REVERT: I 251 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7134 (mp0) REVERT: I 261 ASN cc_start: 0.6562 (t0) cc_final: 0.6266 (m-40) REVERT: I 289 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7718 (mtt180) REVERT: I 297 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7738 (tm-30) REVERT: I 326 LEU cc_start: 0.8365 (mp) cc_final: 0.8134 (mt) REVERT: I 331 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6582 (mt-10) REVERT: I 360 ARG cc_start: 0.4901 (mtp180) cc_final: 0.3241 (mtt90) REVERT: I 400 ASP cc_start: 0.8404 (m-30) cc_final: 0.8081 (m-30) REVERT: J 23 ARG cc_start: 0.7104 (ptt180) cc_final: 0.6563 (ptt180) REVERT: J 60 TYR cc_start: 0.7863 (m-80) cc_final: 0.7481 (m-80) REVERT: J 97 ARG cc_start: 0.7914 (mmt180) cc_final: 0.7644 (mmt180) REVERT: J 155 ARG cc_start: 0.8411 (ptt-90) cc_final: 0.8018 (ptt90) REVERT: J 179 MET cc_start: 0.6763 (tpt) cc_final: 0.6426 (tpt) REVERT: J 192 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7692 (mm-40) REVERT: J 251 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7116 (mp0) REVERT: J 290 MET cc_start: 0.8615 (ttp) cc_final: 0.8378 (ttp) REVERT: J 297 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7793 (tm-30) REVERT: K 21 VAL cc_start: 0.9243 (m) cc_final: 0.9026 (t) REVERT: K 97 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7937 (mmt180) REVERT: K 99 LYS cc_start: 0.7784 (tppp) cc_final: 0.7063 (tptp) REVERT: K 115 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6327 (mt-10) REVERT: K 193 GLU cc_start: 0.7477 (pt0) cc_final: 0.7109 (pt0) REVERT: K 251 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7154 (mp0) REVERT: K 289 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7799 (mtt180) REVERT: K 297 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7706 (tm-30) REVERT: L 15 ARG cc_start: 0.7093 (mtt-85) cc_final: 0.6841 (mmt180) REVERT: L 34 CYS cc_start: 0.8195 (m) cc_final: 0.7948 (m) REVERT: L 60 TYR cc_start: 0.7838 (m-80) cc_final: 0.7105 (m-80) REVERT: L 87 ILE cc_start: 0.8767 (mt) cc_final: 0.8485 (mp) REVERT: L 97 ARG cc_start: 0.7943 (mmt180) cc_final: 0.7726 (mmt180) REVERT: L 192 GLN cc_start: 0.7993 (mm110) cc_final: 0.7791 (mm-40) REVERT: L 219 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7281 (mm) REVERT: L 227 SER cc_start: 0.8472 (m) cc_final: 0.7869 (t) REVERT: L 251 GLU cc_start: 0.7759 (mm-30) cc_final: 0.6968 (mp0) REVERT: L 297 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7617 (tm-30) REVERT: L 384 GLU cc_start: 0.7387 (tp30) cc_final: 0.7125 (tp30) outliers start: 209 outliers final: 160 residues processed: 1038 average time/residue: 0.5219 time to fit residues: 878.8756 Evaluate side-chains 1084 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 894 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 309 SER Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 400 ASP Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 chunk 452 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 355 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 chunk 409 optimal weight: 1.9990 chunk 428 optimal weight: 0.7980 chunk 451 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39948 Z= 0.185 Angle : 0.592 11.316 54132 Z= 0.297 Chirality : 0.044 0.193 6264 Planarity : 0.004 0.039 6972 Dihedral : 4.668 30.336 5467 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.53 % Allowed : 20.73 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 4944 helix: 1.05 (0.12), residues: 1632 sheet: -0.61 (0.14), residues: 1260 loop : -1.03 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.010 0.001 HIS A 90 PHE 0.026 0.001 PHE L 461 TYR 0.011 0.001 TYR E 60 ARG 0.007 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 928 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7618 (mtmm) REVERT: A 60 TYR cc_start: 0.7929 (m-80) cc_final: 0.7275 (m-80) REVERT: A 99 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7073 (tptp) REVERT: A 106 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: A 115 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6499 (tm-30) REVERT: A 192 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7622 (mm110) REVERT: A 219 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7266 (mm) REVERT: A 227 SER cc_start: 0.8194 (m) cc_final: 0.7701 (t) REVERT: A 251 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7151 (mp0) REVERT: A 289 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8109 (mtt180) REVERT: A 297 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 343 MET cc_start: 0.8104 (mmm) cc_final: 0.7773 (mmt) REVERT: A 372 ASN cc_start: 0.5940 (t0) cc_final: 0.5553 (t0) REVERT: A 384 GLU cc_start: 0.7311 (tp30) cc_final: 0.7099 (tp30) REVERT: A 417 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 7 LYS cc_start: 0.4074 (OUTLIER) cc_final: 0.3756 (pttm) REVERT: B 99 LYS cc_start: 0.7688 (tppp) cc_final: 0.7436 (mmmt) REVERT: B 181 MET cc_start: 0.8102 (ptt) cc_final: 0.7344 (tmm) REVERT: B 189 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7249 (t) REVERT: B 192 GLN cc_start: 0.7507 (mm110) cc_final: 0.7099 (mm-40) REVERT: B 219 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6873 (mm) REVERT: B 227 SER cc_start: 0.7883 (m) cc_final: 0.7390 (t) REVERT: B 251 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7006 (mp0) REVERT: B 253 PHE cc_start: 0.8786 (m-80) cc_final: 0.8455 (m-80) REVERT: B 261 ASN cc_start: 0.6512 (t0) cc_final: 0.6266 (m-40) REVERT: B 289 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7115 (mtt180) REVERT: B 326 LEU cc_start: 0.8442 (mp) cc_final: 0.8113 (mt) REVERT: B 348 HIS cc_start: 0.8442 (t-90) cc_final: 0.8216 (t-170) REVERT: B 360 ARG cc_start: 0.4654 (mtp180) cc_final: 0.3664 (mtt90) REVERT: B 398 LEU cc_start: 0.8724 (mp) cc_final: 0.8399 (mp) REVERT: B 427 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7496 (t0) REVERT: C 219 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7693 (mm) REVERT: C 227 SER cc_start: 0.8059 (m) cc_final: 0.7575 (t) REVERT: C 251 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 261 ASN cc_start: 0.6359 (t0) cc_final: 0.5985 (m-40) REVERT: C 270 GLN cc_start: 0.8190 (tp40) cc_final: 0.7686 (tp40) REVERT: C 274 ASP cc_start: 0.8597 (m-30) cc_final: 0.8272 (m-30) REVERT: C 289 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7984 (mtt180) REVERT: C 290 MET cc_start: 0.8596 (ttp) cc_final: 0.8319 (ttp) REVERT: C 297 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 345 HIS cc_start: 0.7017 (p-80) cc_final: 0.6692 (p-80) REVERT: C 384 GLU cc_start: 0.7300 (tp30) cc_final: 0.7037 (tp30) REVERT: C 440 GLU cc_start: 0.6490 (mt-10) cc_final: 0.6192 (tt0) REVERT: D 60 TYR cc_start: 0.7803 (m-80) cc_final: 0.7276 (m-80) REVERT: D 97 ARG cc_start: 0.7863 (mmt180) cc_final: 0.7416 (mmm-85) REVERT: D 127 ASP cc_start: 0.8728 (m-30) cc_final: 0.8390 (m-30) REVERT: D 179 MET cc_start: 0.7170 (tpt) cc_final: 0.6827 (tpt) REVERT: D 181 MET cc_start: 0.8286 (ptt) cc_final: 0.7443 (tmm) REVERT: D 192 GLN cc_start: 0.7826 (mm110) cc_final: 0.7238 (mm-40) REVERT: D 227 SER cc_start: 0.7857 (m) cc_final: 0.7396 (t) REVERT: D 289 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7749 (mtt180) REVERT: D 326 LEU cc_start: 0.8348 (mp) cc_final: 0.8055 (mt) REVERT: D 360 ARG cc_start: 0.4829 (mtp180) cc_final: 0.3254 (mtt-85) REVERT: E 21 VAL cc_start: 0.9225 (m) cc_final: 0.8996 (t) REVERT: E 192 GLN cc_start: 0.8107 (mm110) cc_final: 0.7855 (mm110) REVERT: E 219 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7628 (mm) REVERT: E 251 GLU cc_start: 0.7802 (mm-30) cc_final: 0.6931 (mm-30) REVERT: E 297 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 326 LEU cc_start: 0.8314 (mp) cc_final: 0.8067 (mt) REVERT: F 50 GLU cc_start: 0.7461 (tp30) cc_final: 0.7016 (tp30) REVERT: F 60 TYR cc_start: 0.7855 (m-80) cc_final: 0.7165 (m-80) REVERT: F 97 ARG cc_start: 0.8165 (mmt180) cc_final: 0.7708 (mmt180) REVERT: F 106 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: F 115 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6061 (tm-30) REVERT: F 227 SER cc_start: 0.8096 (m) cc_final: 0.7670 (t) REVERT: F 234 MET cc_start: 0.7128 (mmt) cc_final: 0.6738 (mmt) REVERT: F 251 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7228 (mm-30) REVERT: F 289 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7228 (mtt180) REVERT: F 297 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 331 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6680 (mt-10) REVERT: F 427 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7922 (t0) REVERT: G 6 ARG cc_start: 0.6042 (mtm-85) cc_final: 0.5419 (ptp90) REVERT: G 7 LYS cc_start: 0.4945 (OUTLIER) cc_final: 0.4211 (pttm) REVERT: G 21 VAL cc_start: 0.9183 (m) cc_final: 0.8959 (t) REVERT: G 60 TYR cc_start: 0.8036 (m-80) cc_final: 0.7647 (m-80) REVERT: G 192 GLN cc_start: 0.7599 (mm110) cc_final: 0.7376 (mm110) REVERT: G 193 GLU cc_start: 0.6873 (pt0) cc_final: 0.6638 (pt0) REVERT: G 219 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7154 (mm) REVERT: G 227 SER cc_start: 0.8143 (m) cc_final: 0.7507 (t) REVERT: G 251 GLU cc_start: 0.7897 (mm-30) cc_final: 0.6968 (mp0) REVERT: G 289 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7994 (mtt180) REVERT: G 316 LEU cc_start: 0.8702 (mt) cc_final: 0.8497 (mt) REVERT: G 371 VAL cc_start: 0.8547 (t) cc_final: 0.8264 (m) REVERT: G 372 ASN cc_start: 0.5879 (t0) cc_final: 0.5649 (t0) REVERT: H 60 TYR cc_start: 0.7926 (m-80) cc_final: 0.7376 (m-80) REVERT: H 82 ASN cc_start: 0.8597 (m-40) cc_final: 0.8090 (m-40) REVERT: H 99 LYS cc_start: 0.7817 (ttmm) cc_final: 0.6939 (tptp) REVERT: H 192 GLN cc_start: 0.7877 (mm110) cc_final: 0.7629 (mm-40) REVERT: H 227 SER cc_start: 0.8017 (m) cc_final: 0.7518 (t) REVERT: H 251 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7239 (mp0) REVERT: H 252 GLU cc_start: 0.7707 (tt0) cc_final: 0.7418 (tt0) REVERT: H 289 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7630 (mtt180) REVERT: H 297 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7456 (tm-30) REVERT: H 326 LEU cc_start: 0.8424 (mp) cc_final: 0.8140 (mt) REVERT: H 343 MET cc_start: 0.8269 (mmm) cc_final: 0.8068 (mmm) REVERT: H 427 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7447 (t0) REVERT: I 6 ARG cc_start: 0.5742 (mtm-85) cc_final: 0.5170 (ptp90) REVERT: I 7 LYS cc_start: 0.4757 (OUTLIER) cc_final: 0.4208 (pttm) REVERT: I 46 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7069 (mm) REVERT: I 227 SER cc_start: 0.8170 (m) cc_final: 0.7564 (t) REVERT: I 251 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7155 (mp0) REVERT: I 261 ASN cc_start: 0.6634 (t0) cc_final: 0.6307 (m-40) REVERT: I 289 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7716 (mtt180) REVERT: I 297 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7634 (tm-30) REVERT: I 326 LEU cc_start: 0.8352 (mp) cc_final: 0.8124 (mt) REVERT: I 331 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6520 (mt-10) REVERT: I 360 ARG cc_start: 0.4552 (mtp180) cc_final: 0.2833 (mtt90) REVERT: I 400 ASP cc_start: 0.8384 (m-30) cc_final: 0.8093 (m-30) REVERT: J 21 VAL cc_start: 0.9169 (m) cc_final: 0.8886 (t) REVERT: J 23 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6574 (ptt180) REVERT: J 97 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7596 (mmt180) REVERT: J 155 ARG cc_start: 0.8396 (ptt-90) cc_final: 0.8009 (ptt90) REVERT: J 192 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7563 (mm110) REVERT: J 251 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7058 (mp0) REVERT: J 297 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7788 (tm-30) REVERT: K 21 VAL cc_start: 0.9236 (m) cc_final: 0.9013 (t) REVERT: K 97 ARG cc_start: 0.8203 (mmt180) cc_final: 0.7928 (mmt180) REVERT: K 99 LYS cc_start: 0.7772 (tppp) cc_final: 0.7053 (tptp) REVERT: K 115 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6224 (mt-10) REVERT: K 193 GLU cc_start: 0.7327 (pt0) cc_final: 0.6919 (pt0) REVERT: K 251 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7157 (mp0) REVERT: K 289 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7758 (mtt180) REVERT: K 290 MET cc_start: 0.8622 (ttp) cc_final: 0.8371 (ttp) REVERT: K 297 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7728 (tm-30) REVERT: L 60 TYR cc_start: 0.7800 (m-80) cc_final: 0.7109 (m-80) REVERT: L 87 ILE cc_start: 0.8784 (mt) cc_final: 0.8530 (mp) REVERT: L 192 GLN cc_start: 0.8037 (mm110) cc_final: 0.7820 (mm-40) REVERT: L 219 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7151 (mm) REVERT: L 227 SER cc_start: 0.8441 (m) cc_final: 0.7884 (t) REVERT: L 251 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6921 (mp0) REVERT: L 289 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: L 297 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7548 (tm-30) REVERT: L 384 GLU cc_start: 0.7367 (tp30) cc_final: 0.6981 (tp30) outliers start: 194 outliers final: 151 residues processed: 1053 average time/residue: 0.5386 time to fit residues: 917.6041 Evaluate side-chains 1066 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 888 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 309 SER Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 289 ARG Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 6.9990 chunk 478 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 502 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 chunk 399 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 11 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39948 Z= 0.265 Angle : 0.638 15.483 54132 Z= 0.318 Chirality : 0.046 0.232 6264 Planarity : 0.004 0.041 6972 Dihedral : 4.819 29.586 5464 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.79 % Allowed : 20.75 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 4944 helix: 0.83 (0.12), residues: 1704 sheet: -0.62 (0.14), residues: 1260 loop : -1.05 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 122 HIS 0.010 0.001 HIS A 90 PHE 0.027 0.002 PHE L 461 TYR 0.012 0.001 TYR E 60 ARG 0.010 0.000 ARG H 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 890 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.4162 (OUTLIER) cc_final: 0.3488 (pttm) REVERT: A 55 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7332 (mmtm) REVERT: A 60 TYR cc_start: 0.7990 (m-80) cc_final: 0.7295 (m-80) REVERT: A 99 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7196 (tptp) REVERT: A 115 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 192 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7614 (mm110) REVERT: A 219 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7173 (mm) REVERT: A 227 SER cc_start: 0.8195 (m) cc_final: 0.7698 (t) REVERT: A 250 TYR cc_start: 0.8001 (m-10) cc_final: 0.7514 (m-80) REVERT: A 251 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7178 (mp0) REVERT: A 289 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: A 297 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 343 MET cc_start: 0.8093 (mmm) cc_final: 0.7779 (mmt) REVERT: A 372 ASN cc_start: 0.5942 (t0) cc_final: 0.5596 (t0) REVERT: A 384 GLU cc_start: 0.7368 (tp30) cc_final: 0.7134 (tp30) REVERT: A 417 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 440 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5766 (tt0) REVERT: B 47 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7875 (mmmt) REVERT: B 99 LYS cc_start: 0.7722 (tppp) cc_final: 0.7457 (mmmt) REVERT: B 189 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7222 (t) REVERT: B 192 GLN cc_start: 0.7565 (mm110) cc_final: 0.7139 (mm-40) REVERT: B 219 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6900 (mm) REVERT: B 227 SER cc_start: 0.7851 (m) cc_final: 0.7370 (t) REVERT: B 251 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7030 (mp0) REVERT: B 253 PHE cc_start: 0.8827 (m-80) cc_final: 0.8546 (m-80) REVERT: B 261 ASN cc_start: 0.6415 (t0) cc_final: 0.6150 (m-40) REVERT: B 274 ASP cc_start: 0.8539 (m-30) cc_final: 0.8256 (m-30) REVERT: B 289 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: B 326 LEU cc_start: 0.8433 (mp) cc_final: 0.8112 (mt) REVERT: B 348 HIS cc_start: 0.8431 (t-90) cc_final: 0.8174 (t-170) REVERT: B 360 ARG cc_start: 0.4761 (mtp180) cc_final: 0.3697 (mtt90) REVERT: B 398 LEU cc_start: 0.8831 (mp) cc_final: 0.8492 (mp) REVERT: B 427 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7401 (t0) REVERT: C 192 GLN cc_start: 0.7836 (mm110) cc_final: 0.7513 (mm-40) REVERT: C 219 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7740 (mm) REVERT: C 227 SER cc_start: 0.8061 (m) cc_final: 0.7612 (t) REVERT: C 251 GLU cc_start: 0.7719 (mm-30) cc_final: 0.6986 (mp0) REVERT: C 261 ASN cc_start: 0.6227 (t0) cc_final: 0.5878 (m-40) REVERT: C 274 ASP cc_start: 0.8618 (m-30) cc_final: 0.8276 (m-30) REVERT: C 289 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8180 (mtt180) REVERT: C 290 MET cc_start: 0.8683 (ttp) cc_final: 0.8382 (ttp) REVERT: C 297 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 345 HIS cc_start: 0.7186 (p-80) cc_final: 0.6872 (p-80) REVERT: C 440 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6228 (tt0) REVERT: D 97 ARG cc_start: 0.7914 (mmt180) cc_final: 0.7406 (mmm-85) REVERT: D 179 MET cc_start: 0.7172 (tpt) cc_final: 0.6878 (tpt) REVERT: D 192 GLN cc_start: 0.7794 (mm110) cc_final: 0.7179 (mm-40) REVERT: D 227 SER cc_start: 0.7847 (m) cc_final: 0.7392 (t) REVERT: D 289 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7751 (mtt180) REVERT: D 326 LEU cc_start: 0.8366 (mp) cc_final: 0.8110 (mt) REVERT: D 360 ARG cc_start: 0.4903 (mtp180) cc_final: 0.3278 (mtt-85) REVERT: E 21 VAL cc_start: 0.9234 (m) cc_final: 0.9006 (t) REVERT: E 129 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: E 192 GLN cc_start: 0.8137 (mm110) cc_final: 0.7831 (mm110) REVERT: E 219 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7622 (mm) REVERT: E 251 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7112 (mm-30) REVERT: E 261 ASN cc_start: 0.6608 (m-40) cc_final: 0.6369 (m-40) REVERT: E 326 LEU cc_start: 0.8339 (mp) cc_final: 0.8075 (mt) REVERT: E 384 GLU cc_start: 0.7236 (tp30) cc_final: 0.6998 (tp30) REVERT: F 60 TYR cc_start: 0.7898 (m-80) cc_final: 0.7201 (m-80) REVERT: F 192 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7306 (mm-40) REVERT: F 227 SER cc_start: 0.8059 (m) cc_final: 0.7601 (t) REVERT: F 234 MET cc_start: 0.7073 (mmt) cc_final: 0.6636 (mmt) REVERT: F 251 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7152 (mp0) REVERT: F 289 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7184 (mtt180) REVERT: F 295 ASP cc_start: 0.8805 (t0) cc_final: 0.8518 (t0) REVERT: F 297 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7757 (tm-30) REVERT: F 331 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6702 (mt-10) REVERT: F 427 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7927 (t0) REVERT: F 440 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6285 (tt0) REVERT: G 6 ARG cc_start: 0.6057 (mtm-85) cc_final: 0.5504 (ptp90) REVERT: G 7 LYS cc_start: 0.4984 (OUTLIER) cc_final: 0.4367 (pttm) REVERT: G 21 VAL cc_start: 0.9170 (m) cc_final: 0.8961 (t) REVERT: G 60 TYR cc_start: 0.8057 (m-80) cc_final: 0.7682 (m-80) REVERT: G 192 GLN cc_start: 0.7639 (mm110) cc_final: 0.7308 (mm110) REVERT: G 219 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7104 (mm) REVERT: G 251 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7033 (mp0) REVERT: G 289 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8031 (mtt180) REVERT: G 440 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6167 (tt0) REVERT: H 60 TYR cc_start: 0.7926 (m-80) cc_final: 0.7325 (m-80) REVERT: H 82 ASN cc_start: 0.8527 (m-40) cc_final: 0.8101 (m-40) REVERT: H 99 LYS cc_start: 0.7875 (ttmm) cc_final: 0.6963 (tptp) REVERT: H 192 GLN cc_start: 0.7914 (mm110) cc_final: 0.7606 (mm-40) REVERT: H 227 SER cc_start: 0.8041 (m) cc_final: 0.7523 (t) REVERT: H 250 TYR cc_start: 0.8250 (m-80) cc_final: 0.7754 (m-80) REVERT: H 251 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7258 (mp0) REVERT: H 252 GLU cc_start: 0.7758 (tt0) cc_final: 0.7485 (tt0) REVERT: H 289 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6957 (mtt180) REVERT: H 297 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7698 (tm-30) REVERT: H 326 LEU cc_start: 0.8467 (mp) cc_final: 0.8191 (mt) REVERT: H 427 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7448 (t0) REVERT: I 6 ARG cc_start: 0.5897 (mtm-85) cc_final: 0.5413 (ptp90) REVERT: I 7 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.4344 (pttm) REVERT: I 46 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7176 (mm) REVERT: I 97 ARG cc_start: 0.7991 (mmt180) cc_final: 0.7398 (mmt180) REVERT: I 227 SER cc_start: 0.8153 (m) cc_final: 0.7496 (t) REVERT: I 235 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6818 (mt-10) REVERT: I 251 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7170 (mp0) REVERT: I 261 ASN cc_start: 0.6326 (t0) cc_final: 0.6067 (m-40) REVERT: I 282 LEU cc_start: 0.8675 (tp) cc_final: 0.8442 (tp) REVERT: I 289 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7724 (mtt180) REVERT: I 297 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7672 (tm-30) REVERT: I 326 LEU cc_start: 0.8353 (mp) cc_final: 0.8104 (mt) REVERT: I 331 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6544 (mt-10) REVERT: I 400 ASP cc_start: 0.8380 (m-30) cc_final: 0.8138 (m-30) REVERT: J 21 VAL cc_start: 0.9178 (m) cc_final: 0.8886 (t) REVERT: J 23 ARG cc_start: 0.7093 (ptt180) cc_final: 0.6563 (ptt180) REVERT: J 60 TYR cc_start: 0.7672 (m-80) cc_final: 0.7229 (m-80) REVERT: J 97 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7610 (mmt180) REVERT: J 155 ARG cc_start: 0.8425 (ptt-90) cc_final: 0.8048 (ptt90) REVERT: J 192 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7541 (mm110) REVERT: J 251 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7089 (mp0) REVERT: J 289 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7761 (mtt180) REVERT: J 297 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7795 (tm-30) REVERT: K 21 VAL cc_start: 0.9239 (m) cc_final: 0.9025 (t) REVERT: K 46 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7302 (mm) REVERT: K 97 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7972 (mmt180) REVERT: K 99 LYS cc_start: 0.7801 (tppp) cc_final: 0.7068 (tptp) REVERT: K 115 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6255 (mt-10) REVERT: K 193 GLU cc_start: 0.7266 (pt0) cc_final: 0.6861 (pt0) REVERT: K 251 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7196 (mp0) REVERT: K 289 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7771 (mtt180) REVERT: K 290 MET cc_start: 0.8630 (ttp) cc_final: 0.8362 (ttm) REVERT: K 297 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7760 (tm-30) REVERT: L 60 TYR cc_start: 0.7818 (m-80) cc_final: 0.7049 (m-80) REVERT: L 87 ILE cc_start: 0.8809 (mt) cc_final: 0.8540 (mp) REVERT: L 192 GLN cc_start: 0.8037 (mm110) cc_final: 0.7801 (mm-40) REVERT: L 219 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7197 (mm) REVERT: L 227 SER cc_start: 0.8455 (m) cc_final: 0.7906 (t) REVERT: L 251 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7005 (mp0) REVERT: L 289 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7562 (mtt180) REVERT: L 297 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7652 (tm-30) REVERT: L 384 GLU cc_start: 0.7368 (tp30) cc_final: 0.6956 (tp30) REVERT: L 427 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7391 (m-30) outliers start: 205 outliers final: 160 residues processed: 1014 average time/residue: 0.5410 time to fit residues: 891.7159 Evaluate side-chains 1063 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 874 time to evaluate : 4.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 400 ASP Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 309 SER Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 289 ARG Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 320 SER Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 289 ARG Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 400 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122039 restraints weight = 60416.061| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.82 r_work: 0.3232 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 39948 Z= 0.373 Angle : 0.917 59.195 54132 Z= 0.525 Chirality : 0.049 0.884 6264 Planarity : 0.005 0.091 6972 Dihedral : 4.820 29.514 5464 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.76 % Allowed : 20.89 % Favored : 74.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 4944 helix: 0.83 (0.12), residues: 1704 sheet: -0.61 (0.14), residues: 1260 loop : -1.06 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 122 HIS 0.009 0.001 HIS A 90 PHE 0.024 0.002 PHE L 461 TYR 0.011 0.001 TYR E 60 ARG 0.008 0.000 ARG H 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13469.61 seconds wall clock time: 243 minutes 6.39 seconds (14586.39 seconds total)