Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 06:33:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/05_2023/7u5h_26350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/05_2023/7u5h_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_26350/05_2023/7u5h_26350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/05_2023/7u5h_26350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/05_2023/7u5h_26350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5h_26350/05_2023/7u5h_26350.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 19.66, per 1000 atoms: 0.50 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: 16.56 Conformation dependent library (CDL) restraints added in 6.0 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: 2.49 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: 15.36 Time building geometry restraints manager: 17.56 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.060 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 104.360 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.220 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 5.200 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 outliers start: 228 outliers final: 82 residues processed: 1379 average time/residue: 0.5837 time to fit residues: 1295.4097 Evaluate side-chains 1058 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 976 time to evaluate : 4.618 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.3813 time to fit residues: 65.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 3.9990 chunk 382 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 457 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 432 GLN B 106 GLN B 308 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 192 GLN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 192 GLN K 11 GLN K 148 GLN ** K 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 39948 Z= 0.181 Angle : 0.608 11.073 54132 Z= 0.312 Chirality : 0.045 0.219 6264 Planarity : 0.005 0.046 6972 Dihedral : 4.590 23.018 5436 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 2.92 % 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: -0.24 (0.11), residues: 4944 helix: 1.11 (0.12), residues: 1644 sheet: -0.23 (0.15), residues: 1152 loop : -1.08 (0.11), residues: 2148 *********************** 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 1185 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1060 time to evaluate : 5.114 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 outliers start: 125 outliers final: 52 residues processed: 1134 average time/residue: 0.5228 time to fit residues: 960.6971 Evaluate side-chains 954 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 902 time to evaluate : 4.502 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3626 time to fit residues: 42.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 6.9990 chunk 142 optimal weight: 0.0020 chunk 380 optimal weight: 7.9990 chunk 311 optimal weight: 0.3980 chunk 126 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 495 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 chunk 454 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 367 optimal weight: 10.0000 overall best weight: 2.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 308 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 148 GLN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 296 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 106 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN J 111 GLN J 148 GLN ** J 192 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 296 ASN L 11 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 148 GLN L 296 ASN ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 39948 Z= 0.323 Angle : 0.651 8.393 54132 Z= 0.332 Chirality : 0.047 0.254 6264 Planarity : 0.005 0.034 6972 Dihedral : 4.759 23.251 5436 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 2.19 % 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: -0.39 (0.11), residues: 4944 helix: 1.01 (0.12), residues: 1632 sheet: -0.29 (0.15), residues: 1152 loop : -1.19 (0.12), residues: 2160 *********************** 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 1040 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 946 time to evaluate : 4.507 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 outliers start: 94 outliers final: 59 residues processed: 994 average time/residue: 0.5442 time to fit residues: 871.4273 Evaluate side-chains 927 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 868 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3704 time to fit residues: 48.2649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 460 optimal weight: 3.9990 chunk 487 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 436 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 106 GLN B 296 ASN B 308 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 296 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS J 111 GLN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 39948 Z= 0.265 Angle : 0.616 13.082 54132 Z= 0.314 Chirality : 0.046 0.225 6264 Planarity : 0.004 0.035 6972 Dihedral : 4.671 23.770 5436 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.29 % 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: 0.95 (0.12), residues: 1632 sheet: -0.33 (0.15), residues: 1152 loop : -1.19 (0.12), residues: 2160 *********************** 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 1043 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 945 time to evaluate : 5.303 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 outliers start: 98 outliers final: 53 residues processed: 1001 average time/residue: 0.5540 time to fit residues: 902.7332 Evaluate side-chains 927 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 874 time to evaluate : 4.579 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.3873 time to fit residues: 44.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 0.9990 chunk 276 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 362 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 336 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 437 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 287 HIS D 308 GLN F 110 GLN F 152 HIS G 152 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 HIS ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 HIS ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 39948 Z= 0.179 Angle : 0.576 11.281 54132 Z= 0.295 Chirality : 0.044 0.216 6264 Planarity : 0.004 0.040 6972 Dihedral : 4.451 24.053 5436 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 2.17 % 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: -0.38 (0.11), residues: 4944 helix: 1.06 (0.12), residues: 1632 sheet: -0.38 (0.14), residues: 1152 loop : -1.16 (0.12), residues: 2160 *********************** 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 1067 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 974 time to evaluate : 4.845 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 outliers start: 93 outliers final: 55 residues processed: 1043 average time/residue: 0.5276 time to fit residues: 897.2049 Evaluate side-chains 936 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 881 time to evaluate : 4.643 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.3710 time to fit residues: 44.5560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 7.9990 chunk 438 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 120 optimal weight: 0.2980 chunk 487 optimal weight: 4.9990 chunk 404 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN F 11 GLN F 296 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 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** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 39948 Z= 0.194 Angle : 0.589 13.397 54132 Z= 0.299 Chirality : 0.044 0.198 6264 Planarity : 0.004 0.034 6972 Dihedral : 4.399 23.327 5436 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.89 % 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: -0.36 (0.11), residues: 4944 helix: 1.12 (0.12), residues: 1632 sheet: -0.40 (0.14), residues: 1152 loop : -1.16 (0.12), residues: 2160 *********************** 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 1010 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 929 time to evaluate : 5.260 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 outliers start: 81 outliers final: 41 residues processed: 978 average time/residue: 0.5434 time to fit residues: 864.3108 Evaluate side-chains 912 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 871 time to evaluate : 4.673 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3758 time to fit residues: 35.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 356 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 410 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 485 optimal weight: 1.9990 chunk 304 optimal weight: 6.9990 chunk 296 optimal weight: 0.5980 chunk 224 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 350 ASN D 182 HIS D 192 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN E 148 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 HIS ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN ** L 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 39948 Z= 0.357 Angle : 0.680 12.633 54132 Z= 0.345 Chirality : 0.048 0.229 6264 Planarity : 0.005 0.041 6972 Dihedral : 4.750 23.973 5436 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.73 % 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: -0.59 (0.11), residues: 4944 helix: 0.90 (0.12), residues: 1632 sheet: -0.44 (0.15), residues: 1080 loop : -1.31 (0.12), residues: 2232 *********************** 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 982 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 908 time to evaluate : 4.755 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 outliers start: 74 outliers final: 45 residues processed: 936 average time/residue: 0.5504 time to fit residues: 830.3225 Evaluate side-chains 915 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 870 time to evaluate : 4.678 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3817 time to fit residues: 38.2396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 290 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 308 optimal weight: 0.5980 chunk 330 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 381 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 106 GLN C 296 ASN D 192 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 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** ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 39948 Z= 0.212 Angle : 0.617 11.861 54132 Z= 0.313 Chirality : 0.045 0.219 6264 Planarity : 0.004 0.040 6972 Dihedral : 4.511 25.629 5436 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.91 % 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: -0.52 (0.11), residues: 4944 helix: 0.96 (0.12), residues: 1632 sheet: -0.41 (0.15), residues: 1104 loop : -1.27 (0.12), residues: 2208 *********************** 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 993 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 954 time to evaluate : 4.959 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 outliers start: 39 outliers final: 20 residues processed: 971 average time/residue: 0.5519 time to fit residues: 865.8307 Evaluate side-chains 912 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 892 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4131 time to fit residues: 21.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 0.8980 chunk 465 optimal weight: 0.7980 chunk 424 optimal weight: 3.9990 chunk 452 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 355 optimal weight: 0.0050 chunk 138 optimal weight: 3.9990 chunk 409 optimal weight: 3.9990 chunk 428 optimal weight: 8.9990 chunk 451 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 296 ASN E 296 ASN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN L 380 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3124 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= 0.197 Angle : 0.622 14.047 54132 Z= 0.314 Chirality : 0.045 0.201 6264 Planarity : 0.004 0.038 6972 Dihedral : 4.469 28.683 5436 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.07 % 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: -0.48 (0.11), residues: 4944 helix: 1.01 (0.12), residues: 1632 sheet: -0.63 (0.14), residues: 1248 loop : -1.12 (0.13), residues: 2064 *********************** 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 968 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 922 time to evaluate : 5.214 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 outliers start: 46 outliers final: 24 residues processed: 942 average time/residue: 0.5543 time to fit residues: 841.5431 Evaluate side-chains 891 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 867 time to evaluate : 4.945 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3856 time to fit residues: 24.0558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 332 optimal weight: 0.3980 chunk 502 optimal weight: 4.9990 chunk 462 optimal weight: 7.9990 chunk 399 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 308 optimal weight: 0.4980 chunk 245 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN D 192 GLN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 39948 Z= 0.246 Angle : 0.659 14.842 54132 Z= 0.331 Chirality : 0.046 0.218 6264 Planarity : 0.005 0.041 6972 Dihedral : 4.545 28.180 5436 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.23 % 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: -0.55 (0.11), residues: 4944 helix: 0.94 (0.12), residues: 1632 sheet: -0.70 (0.14), residues: 1224 loop : -1.13 (0.13), residues: 2088 ********************** 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 895 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 885 time to evaluate : 4.782 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 outliers start: 10 outliers final: 7 residues processed: 887 average time/residue: 0.5537 time to fit residues: 795.8937 Evaluate side-chains 872 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 865 time to evaluate : 3.664 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3546 time to fit residues: 10.1295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 0.9990 chunk 425 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 368 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 400 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 411 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: