Starting phenix.real_space_refine on Mon Feb 19 02:07:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5i_26351/02_2024/7u5i_26351.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14688 2.51 5 N 4280 2.21 5 O 4451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23539 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "D" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "E" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "F" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "G" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "H" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 12.14, per 1000 atoms: 0.52 Number of scatterers: 23539 At special positions: 0 Unit cell: (133.75, 133.75, 103.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4451 8.00 N 4280 7.00 C 14688 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: 9.84 Conformation dependent library (CDL) restraints added in 4.6 seconds 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 43.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 93 " --> pdb=" O CYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 118 through 130 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 403 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 130 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.512A pdb=" N ASP B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 403 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY C 93 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 130 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.568A pdb=" N LEU C 348 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 403 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 68 through 77 removed outlier: 4.735A pdb=" N ASP D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY D 93 " --> pdb=" O CYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 130 Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.510A pdb=" N ASP D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 348 removed outlier: 3.568A pdb=" N LEU D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 403 Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 96 removed outlier: 5.009A pdb=" N THR E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY E 93 " --> pdb=" O CYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 130 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 223 Processing helix chain 'E' and resid 232 through 239 Processing helix chain 'E' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU E 348 " --> pdb=" O ILE E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 403 Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 5.009A pdb=" N THR F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY F 93 " --> pdb=" O CYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 130 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 Processing helix chain 'F' and resid 232 through 239 Processing helix chain 'F' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.510A pdb=" N ASP F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 403 Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 61 through 67 Processing helix chain 'G' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY G 93 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 130 Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 223 Processing helix chain 'G' and resid 232 through 239 Processing helix chain 'G' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU G 348 " --> pdb=" O ILE G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 403 Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 61 through 67 Processing helix chain 'H' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY H 93 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 130 Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 223 Processing helix chain 'H' and resid 232 through 239 Processing helix chain 'H' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL H 282 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP H 338 " --> pdb=" O LEU H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY A 249 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A 258 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS A 329 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER A 162 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 327 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY B 249 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE B 258 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS B 329 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B 162 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY B 327 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY C 249 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE C 258 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS C 329 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER C 162 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY C 327 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY D 249 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE D 258 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS D 329 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER D 162 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY D 327 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY E 249 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE E 258 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS E 329 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER E 162 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY E 327 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY F 249 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE F 258 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS F 329 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER F 162 " --> pdb=" O GLY F 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY F 327 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY G 249 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE G 258 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS G 329 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER G 162 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY G 327 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY H 249 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE H 258 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS H 329 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER H 162 " --> pdb=" O GLY H 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY H 327 " --> pdb=" O SER H 162 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2904 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: 7.13 Time building geometry restraints manager: 10.64 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: 6184 1.33 - 1.45: 4173 1.45 - 1.57: 13371 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 23912 Sorted by residual: bond pdb=" CA THR H 80 " pdb=" C THR H 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.26e+00 bond pdb=" CA THR E 80 " pdb=" C THR E 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.23e+00 bond pdb=" CA THR F 80 " pdb=" C THR F 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.02e+00 bond pdb=" CA THR G 80 " pdb=" C THR G 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.02e+00 bond pdb=" CA THR C 80 " pdb=" C THR C 80 " ideal model delta sigma weight residual 1.527 1.497 0.029 1.32e-02 5.74e+03 4.99e+00 ... (remaining 23907 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.27: 976 107.27 - 114.00: 13206 114.00 - 120.73: 9999 120.73 - 127.47: 7827 127.47 - 134.20: 296 Bond angle restraints: 32304 Sorted by residual: angle pdb=" C THR G 166 " pdb=" CA THR G 166 " pdb=" CB THR G 166 " ideal model delta sigma weight residual 111.95 103.36 8.59 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR F 166 " pdb=" CA THR F 166 " pdb=" CB THR F 166 " ideal model delta sigma weight residual 111.95 103.36 8.59 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR E 166 " pdb=" CA THR E 166 " pdb=" CB THR E 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR A 166 " pdb=" CA THR A 166 " pdb=" CB THR A 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR B 166 " pdb=" CA THR B 166 " pdb=" CB THR B 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 ... (remaining 32299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 13440 16.15 - 32.30: 824 32.30 - 48.45: 240 48.45 - 64.61: 48 64.61 - 80.76: 16 Dihedral angle restraints: 14568 sinusoidal: 6224 harmonic: 8344 Sorted by residual: dihedral pdb=" N ARG B 205 " pdb=" CA ARG B 205 " pdb=" CB ARG B 205 " pdb=" CG ARG B 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.04 59.04 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG H 205 " pdb=" CA ARG H 205 " pdb=" CB ARG H 205 " pdb=" CG ARG H 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG C 205 " pdb=" CA ARG C 205 " pdb=" CB ARG C 205 " pdb=" CG ARG C 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 14565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2803 0.050 - 0.100: 560 0.100 - 0.150: 101 0.150 - 0.200: 0 0.200 - 0.250: 8 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA THR B 82 " pdb=" N THR B 82 " pdb=" C THR B 82 " pdb=" CB THR B 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA THR D 82 " pdb=" N THR D 82 " pdb=" C THR D 82 " pdb=" CB THR D 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA THR H 82 " pdb=" N THR H 82 " pdb=" C THR H 82 " pdb=" CB THR H 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3469 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO D 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 80 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO E 81 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO F 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.041 5.00e-02 4.00e+02 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3112 2.76 - 3.29: 23296 3.29 - 3.83: 41535 3.83 - 4.36: 48904 4.36 - 4.90: 83235 Nonbonded interactions: 200082 Sorted by model distance: nonbonded pdb=" OD2 ASP F 223 " pdb=" O HOH F 501 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP B 223 " pdb=" O HOH B 501 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP H 223 " pdb=" O HOH H 501 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP E 223 " pdb=" O HOH E 501 " model vdw 2.222 2.440 nonbonded pdb=" OD2 ASP G 223 " pdb=" O HOH G 501 " model vdw 2.223 2.440 ... (remaining 200077 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.020 Extract box with map and model: 4.960 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 61.530 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 : 0.002 0.037 23912 Z= 0.163 Angle : 0.557 8.590 32304 Z= 0.306 Chirality : 0.042 0.250 3472 Planarity : 0.005 0.073 4248 Dihedral : 11.618 80.757 9192 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.82 % Allowed : 5.64 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 2872 helix: 2.02 (0.16), residues: 1096 sheet: 0.11 (0.24), residues: 432 loop : -0.46 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 84 HIS 0.002 0.000 HIS G 66 PHE 0.010 0.001 PHE G 286 TYR 0.003 0.001 TYR H 207 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 735 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7500 (t0) cc_final: 0.7202 (t0) REVERT: A 148 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7886 (mtpt) REVERT: A 227 PHE cc_start: 0.7874 (p90) cc_final: 0.7476 (p90) REVERT: A 279 MET cc_start: 0.8406 (mmm) cc_final: 0.8028 (mmm) REVERT: A 280 LYS cc_start: 0.7844 (ptpp) cc_final: 0.7638 (ptpp) REVERT: A 281 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7487 (ptmm) REVERT: A 298 GLN cc_start: 0.7884 (mt0) cc_final: 0.7585 (mt0) REVERT: A 324 LEU cc_start: 0.8715 (tp) cc_final: 0.7913 (tp) REVERT: A 325 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7384 (ttt180) REVERT: A 346 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 352 LYS cc_start: 0.7511 (tmtt) cc_final: 0.7226 (tmtt) REVERT: A 381 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 134 ASP cc_start: 0.7486 (t0) cc_final: 0.7194 (t0) REVERT: B 148 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7894 (mtpt) REVERT: B 227 PHE cc_start: 0.7829 (p90) cc_final: 0.7420 (p90) REVERT: B 279 MET cc_start: 0.8396 (mmm) cc_final: 0.8033 (mmm) REVERT: B 281 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7465 (ptmm) REVERT: B 298 GLN cc_start: 0.7908 (mt0) cc_final: 0.7586 (mt0) REVERT: B 324 LEU cc_start: 0.8712 (tp) cc_final: 0.7897 (tp) REVERT: B 325 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7383 (ttt180) REVERT: B 344 ILE cc_start: 0.8526 (mt) cc_final: 0.8293 (mt) REVERT: B 346 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 352 LYS cc_start: 0.7497 (tmtt) cc_final: 0.7219 (tmtt) REVERT: B 381 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 134 ASP cc_start: 0.7503 (t0) cc_final: 0.7210 (t0) REVERT: C 148 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7871 (mtpt) REVERT: C 227 PHE cc_start: 0.7830 (p90) cc_final: 0.7432 (p90) REVERT: C 279 MET cc_start: 0.8398 (mmm) cc_final: 0.8032 (mmm) REVERT: C 281 LYS cc_start: 0.7769 (ptmt) cc_final: 0.7472 (ptmm) REVERT: C 298 GLN cc_start: 0.7907 (mt0) cc_final: 0.7574 (mt0) REVERT: C 324 LEU cc_start: 0.8714 (tp) cc_final: 0.7897 (tp) REVERT: C 325 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7379 (ttt180) REVERT: C 346 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 352 LYS cc_start: 0.7478 (tmtt) cc_final: 0.7210 (tmtt) REVERT: C 381 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 134 ASP cc_start: 0.7513 (t0) cc_final: 0.7199 (t0) REVERT: D 148 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7801 (mtpt) REVERT: D 227 PHE cc_start: 0.7830 (p90) cc_final: 0.7422 (p90) REVERT: D 279 MET cc_start: 0.8397 (mmm) cc_final: 0.8030 (mmm) REVERT: D 281 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7465 (ptmm) REVERT: D 298 GLN cc_start: 0.7923 (mt0) cc_final: 0.7612 (mt0) REVERT: D 324 LEU cc_start: 0.8714 (tp) cc_final: 0.7897 (tp) REVERT: D 325 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7389 (ttt180) REVERT: D 346 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7316 (tm-30) REVERT: D 352 LYS cc_start: 0.7497 (tmtt) cc_final: 0.7222 (tmtt) REVERT: D 381 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7261 (mt-10) REVERT: E 134 ASP cc_start: 0.7555 (t0) cc_final: 0.7270 (t0) REVERT: E 227 PHE cc_start: 0.7814 (p90) cc_final: 0.7395 (p90) REVERT: E 279 MET cc_start: 0.8432 (mmm) cc_final: 0.8040 (mmm) REVERT: E 280 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7575 (ptpp) REVERT: E 281 LYS cc_start: 0.7761 (ptmt) cc_final: 0.7466 (ptmm) REVERT: E 298 GLN cc_start: 0.7941 (mt0) cc_final: 0.7632 (mt0) REVERT: E 324 LEU cc_start: 0.8705 (tp) cc_final: 0.7869 (tp) REVERT: E 325 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.7430 (ttt180) REVERT: E 346 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7296 (tm-30) REVERT: E 352 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7240 (tmtt) REVERT: E 381 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7280 (mt-10) REVERT: F 134 ASP cc_start: 0.7533 (t0) cc_final: 0.7261 (t0) REVERT: F 227 PHE cc_start: 0.7817 (p90) cc_final: 0.7404 (p90) REVERT: F 279 MET cc_start: 0.8430 (mmm) cc_final: 0.8041 (mmm) REVERT: F 280 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7596 (ptpp) REVERT: F 281 LYS cc_start: 0.7744 (ptmt) cc_final: 0.7447 (ptmm) REVERT: F 298 GLN cc_start: 0.7908 (mt0) cc_final: 0.7590 (mt0) REVERT: F 324 LEU cc_start: 0.8704 (tp) cc_final: 0.7862 (tp) REVERT: F 325 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7426 (ttt180) REVERT: F 346 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7337 (tm-30) REVERT: F 352 LYS cc_start: 0.7534 (tmtt) cc_final: 0.7249 (tmtt) REVERT: F 381 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7268 (mt-10) REVERT: G 134 ASP cc_start: 0.7556 (t0) cc_final: 0.7249 (t0) REVERT: G 148 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7818 (mtpt) REVERT: G 227 PHE cc_start: 0.7816 (p90) cc_final: 0.7398 (p90) REVERT: G 279 MET cc_start: 0.8430 (mmm) cc_final: 0.8040 (mmm) REVERT: G 280 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7578 (ptpp) REVERT: G 281 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7452 (ptmm) REVERT: G 298 GLN cc_start: 0.7923 (mt0) cc_final: 0.7618 (mt0) REVERT: G 324 LEU cc_start: 0.8704 (tp) cc_final: 0.7864 (tp) REVERT: G 325 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7431 (ttt180) REVERT: G 346 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7338 (tm-30) REVERT: G 352 LYS cc_start: 0.7535 (tmtt) cc_final: 0.7250 (tmtt) REVERT: G 381 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7271 (mt-10) REVERT: H 134 ASP cc_start: 0.7548 (t0) cc_final: 0.7260 (t0) REVERT: H 227 PHE cc_start: 0.7819 (p90) cc_final: 0.7407 (p90) REVERT: H 279 MET cc_start: 0.8431 (mmm) cc_final: 0.8043 (mmm) REVERT: H 280 LYS cc_start: 0.7820 (ptpp) cc_final: 0.7595 (ptpp) REVERT: H 281 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7455 (ptmm) REVERT: H 298 GLN cc_start: 0.7907 (mt0) cc_final: 0.7577 (mt0) REVERT: H 324 LEU cc_start: 0.8706 (tp) cc_final: 0.7863 (tp) REVERT: H 325 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.7422 (ttt180) REVERT: H 346 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 352 LYS cc_start: 0.7518 (tmtt) cc_final: 0.7240 (tmtt) REVERT: H 381 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7284 (mt-10) outliers start: 72 outliers final: 24 residues processed: 776 average time/residue: 0.4339 time to fit residues: 476.9966 Evaluate side-chains 571 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 547 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 408 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 0.0270 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 131 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 131 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 131 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 131 ASN ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 131 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN G 131 ASN ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN H 131 ASN ** H 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23912 Z= 0.267 Angle : 0.582 6.189 32304 Z= 0.310 Chirality : 0.044 0.140 3472 Planarity : 0.005 0.048 4248 Dihedral : 5.189 53.815 3296 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.25 % Allowed : 9.84 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2872 helix: 1.85 (0.16), residues: 1112 sheet: 0.05 (0.24), residues: 448 loop : -0.67 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 84 HIS 0.005 0.001 HIS B 99 PHE 0.018 0.002 PHE C 225 TYR 0.008 0.001 TYR C 207 ARG 0.004 0.000 ARG H 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 597 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8064 (mtmt) REVERT: A 240 MET cc_start: 0.7337 (mtt) cc_final: 0.7108 (mtt) REVERT: A 250 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 280 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7591 (ptpp) REVERT: A 281 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7567 (ptmm) REVERT: A 298 GLN cc_start: 0.8033 (mt0) cc_final: 0.7668 (mt0) REVERT: A 324 LEU cc_start: 0.8671 (tp) cc_final: 0.7947 (tp) REVERT: A 325 ARG cc_start: 0.7716 (ttt-90) cc_final: 0.7297 (ttt180) REVERT: A 344 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 346 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 352 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7178 (tmtt) REVERT: B 127 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7417 (tt0) REVERT: B 240 MET cc_start: 0.7387 (mtt) cc_final: 0.7158 (mtt) REVERT: B 250 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8236 (tp) REVERT: B 281 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7580 (ptmm) REVERT: B 291 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7621 (pttp) REVERT: B 298 GLN cc_start: 0.7995 (mt0) cc_final: 0.7626 (mt0) REVERT: B 324 LEU cc_start: 0.8671 (tp) cc_final: 0.7951 (tp) REVERT: B 325 ARG cc_start: 0.7720 (ttt-90) cc_final: 0.7298 (ttt180) REVERT: B 346 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 352 LYS cc_start: 0.7599 (tmtt) cc_final: 0.7198 (tmtt) REVERT: C 240 MET cc_start: 0.7388 (mtt) cc_final: 0.7157 (mtt) REVERT: C 250 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 281 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7591 (ptmm) REVERT: C 291 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7632 (pttp) REVERT: C 298 GLN cc_start: 0.7998 (mt0) cc_final: 0.7614 (mt0) REVERT: C 324 LEU cc_start: 0.8671 (tp) cc_final: 0.7950 (tp) REVERT: C 325 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7293 (ttt180) REVERT: C 344 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8398 (mp) REVERT: C 346 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 352 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7183 (tmtt) REVERT: D 148 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7884 (mttt) REVERT: D 240 MET cc_start: 0.7386 (mtt) cc_final: 0.7155 (mtt) REVERT: D 250 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8239 (tp) REVERT: D 281 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7583 (ptmm) REVERT: D 298 GLN cc_start: 0.8009 (mt0) cc_final: 0.7656 (mt0) REVERT: D 324 LEU cc_start: 0.8669 (tp) cc_final: 0.7951 (tp) REVERT: D 325 ARG cc_start: 0.7714 (ttt-90) cc_final: 0.7300 (ttt180) REVERT: D 344 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 346 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 352 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7194 (tmtt) REVERT: E 148 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8062 (mtmt) REVERT: E 240 MET cc_start: 0.7364 (mtt) cc_final: 0.7126 (mtt) REVERT: E 250 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8218 (tp) REVERT: E 280 LYS cc_start: 0.7802 (ptpp) cc_final: 0.7584 (ptpp) REVERT: E 281 LYS cc_start: 0.7799 (ptmt) cc_final: 0.7566 (ptmm) REVERT: E 298 GLN cc_start: 0.7999 (mt0) cc_final: 0.7646 (mt0) REVERT: E 324 LEU cc_start: 0.8657 (tp) cc_final: 0.7934 (tp) REVERT: E 325 ARG cc_start: 0.7713 (ttt-90) cc_final: 0.7292 (ttt180) REVERT: E 344 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (mp) REVERT: E 346 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 352 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7194 (tmtt) REVERT: F 240 MET cc_start: 0.7359 (mtt) cc_final: 0.7120 (mtt) REVERT: F 250 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8217 (tp) REVERT: F 280 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7582 (ptpp) REVERT: F 281 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7553 (ptmm) REVERT: F 291 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7625 (pttp) REVERT: F 298 GLN cc_start: 0.7964 (mt0) cc_final: 0.7599 (mt0) REVERT: F 325 ARG cc_start: 0.7709 (ttt-90) cc_final: 0.7393 (ttt180) REVERT: F 344 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8330 (mp) REVERT: F 346 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7342 (tm-30) REVERT: F 352 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7207 (tmtt) REVERT: G 148 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7885 (mttt) REVERT: G 240 MET cc_start: 0.7362 (mtt) cc_final: 0.7128 (mtt) REVERT: G 250 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8212 (tp) REVERT: G 280 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7583 (ptpp) REVERT: G 281 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7557 (ptmm) REVERT: G 298 GLN cc_start: 0.7979 (mt0) cc_final: 0.7631 (mt0) REVERT: G 325 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7399 (ttt180) REVERT: G 344 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8333 (mp) REVERT: G 346 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7342 (tm-30) REVERT: G 352 LYS cc_start: 0.7609 (tmtt) cc_final: 0.7209 (tmtt) REVERT: H 240 MET cc_start: 0.7365 (mtt) cc_final: 0.7129 (mtt) REVERT: H 250 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8211 (tp) REVERT: H 280 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7584 (ptpp) REVERT: H 281 LYS cc_start: 0.7794 (ptmt) cc_final: 0.7562 (ptmm) REVERT: H 291 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7637 (pttp) REVERT: H 298 GLN cc_start: 0.7996 (mt0) cc_final: 0.7615 (mt0) REVERT: H 325 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7391 (ttt180) REVERT: H 344 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8322 (mp) REVERT: H 346 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7328 (tm-30) REVERT: H 352 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7200 (tmtt) outliers start: 83 outliers final: 39 residues processed: 648 average time/residue: 0.4397 time to fit residues: 407.5505 Evaluate side-chains 608 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 554 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 217 optimal weight: 0.2980 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 391 ASN B 391 ASN ** C 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 391 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN E 391 ASN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 GLN ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 GLN G 391 ASN ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 GLN H 391 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23912 Z= 0.295 Angle : 0.613 7.218 32304 Z= 0.320 Chirality : 0.044 0.143 3472 Planarity : 0.005 0.037 4248 Dihedral : 5.157 49.941 3282 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.23 % Allowed : 13.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2872 helix: 1.68 (0.15), residues: 1112 sheet: -0.05 (0.23), residues: 448 loop : -0.80 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS B 99 PHE 0.018 0.002 PHE B 227 TYR 0.013 0.001 TYR C 207 ARG 0.005 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 615 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8330 (m-30) cc_final: 0.8012 (t0) REVERT: A 96 ASN cc_start: 0.8138 (m110) cc_final: 0.7869 (m-40) REVERT: A 111 ASP cc_start: 0.7991 (m-30) cc_final: 0.7788 (m-30) REVERT: A 116 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 127 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: A 148 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8126 (mtmt) REVERT: A 165 ARG cc_start: 0.6998 (ttp80) cc_final: 0.6339 (ttp80) REVERT: A 225 PHE cc_start: 0.7983 (m-10) cc_final: 0.7764 (m-80) REVERT: A 250 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 281 LYS cc_start: 0.7796 (ptmt) cc_final: 0.7574 (ptmm) REVERT: A 298 GLN cc_start: 0.8021 (mt0) cc_final: 0.7606 (mt0) REVERT: A 300 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7808 (tpt90) REVERT: A 325 ARG cc_start: 0.7596 (ttt-90) cc_final: 0.7344 (ttt180) REVERT: A 331 LYS cc_start: 0.6979 (ptmt) cc_final: 0.6076 (tttm) REVERT: A 344 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 346 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 352 LYS cc_start: 0.7544 (tmtt) cc_final: 0.7125 (tmtt) REVERT: B 127 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: B 225 PHE cc_start: 0.7990 (m-10) cc_final: 0.7765 (m-80) REVERT: B 250 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 281 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7609 (ptmm) REVERT: B 298 GLN cc_start: 0.8025 (mt0) cc_final: 0.7589 (mt0) REVERT: B 300 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7808 (tpt90) REVERT: B 331 LYS cc_start: 0.6878 (ptmt) cc_final: 0.5967 (tttm) REVERT: B 346 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 352 LYS cc_start: 0.7589 (tmtt) cc_final: 0.7155 (tmtt) REVERT: C 165 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6339 (ttp80) REVERT: C 208 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7575 (mtt90) REVERT: C 225 PHE cc_start: 0.7995 (m-10) cc_final: 0.7767 (m-80) REVERT: C 250 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8177 (tp) REVERT: C 281 LYS cc_start: 0.7841 (ptmt) cc_final: 0.7617 (ptmm) REVERT: C 298 GLN cc_start: 0.7955 (mt0) cc_final: 0.7512 (mt0) REVERT: C 300 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7817 (tpt90) REVERT: C 325 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.7342 (ttt180) REVERT: C 331 LYS cc_start: 0.6927 (ptmt) cc_final: 0.6043 (tttm) REVERT: C 344 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 346 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 352 LYS cc_start: 0.7521 (tmtt) cc_final: 0.7112 (tmtt) REVERT: D 96 ASN cc_start: 0.8152 (m110) cc_final: 0.7873 (m-40) REVERT: D 148 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8105 (mtmt) REVERT: D 208 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7475 (mtt90) REVERT: D 225 PHE cc_start: 0.7976 (m-10) cc_final: 0.7756 (m-80) REVERT: D 250 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8185 (tp) REVERT: D 281 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7580 (ptmm) REVERT: D 298 GLN cc_start: 0.8034 (mt0) cc_final: 0.7622 (mt0) REVERT: D 300 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7795 (tpt90) REVERT: D 325 ARG cc_start: 0.7578 (ttt-90) cc_final: 0.7376 (ttt180) REVERT: D 344 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 346 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7352 (tm-30) REVERT: D 352 LYS cc_start: 0.7541 (tmtt) cc_final: 0.7123 (tmtt) REVERT: E 96 ASN cc_start: 0.8143 (m110) cc_final: 0.7872 (m-40) REVERT: E 127 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: E 148 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8140 (mtmt) REVERT: E 225 PHE cc_start: 0.7984 (m-10) cc_final: 0.7770 (m-80) REVERT: E 250 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8181 (tp) REVERT: E 280 LYS cc_start: 0.7729 (ptpp) cc_final: 0.7510 (ptpp) REVERT: E 281 LYS cc_start: 0.7775 (ptmt) cc_final: 0.7556 (ptmm) REVERT: E 298 GLN cc_start: 0.7975 (mt0) cc_final: 0.7571 (mt0) REVERT: E 300 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7797 (tpt90) REVERT: E 331 LYS cc_start: 0.6939 (ptmt) cc_final: 0.6026 (tttm) REVERT: E 344 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8355 (mp) REVERT: E 346 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7319 (tm-30) REVERT: E 352 LYS cc_start: 0.7537 (tmtt) cc_final: 0.7110 (tmtt) REVERT: F 95 ASP cc_start: 0.8332 (m-30) cc_final: 0.7990 (t0) REVERT: F 96 ASN cc_start: 0.8149 (m110) cc_final: 0.7887 (m-40) REVERT: F 127 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: F 225 PHE cc_start: 0.7978 (m-10) cc_final: 0.7759 (m-80) REVERT: F 250 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8179 (tp) REVERT: F 280 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7520 (ptpp) REVERT: F 281 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7569 (ptmm) REVERT: F 298 GLN cc_start: 0.7902 (mt0) cc_final: 0.7497 (mt0) REVERT: F 300 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7802 (tpt90) REVERT: F 331 LYS cc_start: 0.6831 (ptmt) cc_final: 0.5980 (tttm) REVERT: F 344 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8355 (mp) REVERT: F 346 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7352 (tm-30) REVERT: F 352 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7125 (tmtt) REVERT: G 95 ASP cc_start: 0.8333 (m-30) cc_final: 0.7981 (t0) REVERT: G 96 ASN cc_start: 0.8156 (m110) cc_final: 0.7867 (m-40) REVERT: G 127 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: G 148 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8106 (mtmt) REVERT: G 208 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7467 (mtt90) REVERT: G 225 PHE cc_start: 0.7978 (m-10) cc_final: 0.7766 (m-80) REVERT: G 250 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8190 (tp) REVERT: G 280 LYS cc_start: 0.7729 (ptpp) cc_final: 0.7510 (ptpp) REVERT: G 281 LYS cc_start: 0.7767 (ptmt) cc_final: 0.7545 (ptmm) REVERT: G 298 GLN cc_start: 0.7915 (mt0) cc_final: 0.7530 (mt0) REVERT: G 344 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8360 (mp) REVERT: G 346 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7354 (tm-30) REVERT: G 352 LYS cc_start: 0.7555 (tmtt) cc_final: 0.7131 (tmtt) REVERT: H 95 ASP cc_start: 0.8335 (m-30) cc_final: 0.7989 (t0) REVERT: H 96 ASN cc_start: 0.8155 (m110) cc_final: 0.7860 (m-40) REVERT: H 225 PHE cc_start: 0.7977 (m-10) cc_final: 0.7760 (m-80) REVERT: H 250 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8174 (tp) REVERT: H 280 LYS cc_start: 0.7737 (ptpp) cc_final: 0.7518 (ptpp) REVERT: H 281 LYS cc_start: 0.7796 (ptmt) cc_final: 0.7577 (ptmm) REVERT: H 298 GLN cc_start: 0.7906 (mt0) cc_final: 0.7486 (mt0) REVERT: H 300 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7813 (tpt90) REVERT: H 331 LYS cc_start: 0.6247 (pttt) cc_final: 0.5486 (tttm) REVERT: H 344 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8347 (mp) REVERT: H 346 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7341 (tm-30) REVERT: H 352 LYS cc_start: 0.7536 (tmtt) cc_final: 0.7120 (tmtt) outliers start: 108 outliers final: 31 residues processed: 666 average time/residue: 0.4590 time to fit residues: 432.7568 Evaluate side-chains 631 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 580 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 344 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 0.0570 chunk 278 optimal weight: 0.9980 chunk 137 optimal weight: 0.0270 chunk 249 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23912 Z= 0.184 Angle : 0.572 6.155 32304 Z= 0.298 Chirality : 0.042 0.157 3472 Planarity : 0.004 0.038 4248 Dihedral : 4.434 36.981 3266 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.78 % Allowed : 16.85 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2872 helix: 1.78 (0.16), residues: 1112 sheet: -0.01 (0.23), residues: 448 loop : -0.78 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.004 0.001 HIS D 99 PHE 0.018 0.002 PHE C 227 TYR 0.007 0.001 TYR C 207 ARG 0.006 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 590 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8291 (m-30) cc_final: 0.7961 (t0) REVERT: A 111 ASP cc_start: 0.8023 (m-30) cc_final: 0.7786 (m-30) REVERT: A 116 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7186 (tm-30) REVERT: A 127 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 148 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8141 (mtmt) REVERT: A 183 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 225 PHE cc_start: 0.8045 (m-10) cc_final: 0.7821 (m-80) REVERT: A 250 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8132 (tp) REVERT: A 281 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7593 (ptmm) REVERT: A 298 GLN cc_start: 0.8014 (mt0) cc_final: 0.7693 (mt0) REVERT: A 300 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7796 (tpt90) REVERT: A 331 LYS cc_start: 0.7202 (ptmt) cc_final: 0.6351 (tttm) REVERT: A 344 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 346 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 352 LYS cc_start: 0.7466 (tmtt) cc_final: 0.6998 (tmtt) REVERT: B 127 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: B 183 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 250 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8140 (tp) REVERT: B 281 LYS cc_start: 0.7788 (ptmt) cc_final: 0.7577 (ptmm) REVERT: B 298 GLN cc_start: 0.8053 (mt0) cc_final: 0.7704 (mt0) REVERT: B 300 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7800 (tpt90) REVERT: B 331 LYS cc_start: 0.6978 (ptmt) cc_final: 0.6095 (tttm) REVERT: B 346 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 352 LYS cc_start: 0.7449 (tmtt) cc_final: 0.6992 (tmtt) REVERT: C 127 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: C 183 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 250 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (tp) REVERT: C 281 LYS cc_start: 0.7796 (ptmt) cc_final: 0.7588 (ptmm) REVERT: C 298 GLN cc_start: 0.7980 (mt0) cc_final: 0.7640 (mt0) REVERT: C 300 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7815 (tpt90) REVERT: C 331 LYS cc_start: 0.7193 (ptmt) cc_final: 0.6351 (tttm) REVERT: C 344 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (mp) REVERT: C 346 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 352 LYS cc_start: 0.7463 (tmtt) cc_final: 0.7003 (tmtt) REVERT: D 95 ASP cc_start: 0.8308 (m-30) cc_final: 0.8013 (t0) REVERT: D 127 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: D 148 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8150 (mttt) REVERT: D 183 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7895 (mt-10) REVERT: D 250 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (tp) REVERT: D 281 LYS cc_start: 0.7758 (ptmt) cc_final: 0.7550 (ptmm) REVERT: D 298 GLN cc_start: 0.8061 (mt0) cc_final: 0.7732 (mt0) REVERT: D 300 ARG cc_start: 0.8037 (tpp80) cc_final: 0.7799 (tpt90) REVERT: D 331 LYS cc_start: 0.7004 (ptmt) cc_final: 0.6169 (tttm) REVERT: D 344 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 346 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 352 LYS cc_start: 0.7493 (tmtt) cc_final: 0.7026 (tmtt) REVERT: E 127 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: E 148 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8128 (mtmt) REVERT: E 183 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7909 (mt-10) REVERT: E 250 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8153 (tp) REVERT: E 298 GLN cc_start: 0.8009 (mt0) cc_final: 0.7653 (mt0) REVERT: E 300 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7817 (tpt90) REVERT: E 331 LYS cc_start: 0.7171 (ptmt) cc_final: 0.6361 (tttm) REVERT: E 344 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8343 (mp) REVERT: E 346 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7360 (tm-30) REVERT: E 352 LYS cc_start: 0.7517 (tmtt) cc_final: 0.7043 (tmtt) REVERT: F 95 ASP cc_start: 0.8288 (m-30) cc_final: 0.7956 (t0) REVERT: F 127 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: F 250 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (tp) REVERT: F 298 GLN cc_start: 0.7977 (mt0) cc_final: 0.7609 (mt0) REVERT: F 300 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7784 (tpt90) REVERT: F 331 LYS cc_start: 0.6932 (ptmt) cc_final: 0.6105 (tttm) REVERT: F 344 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8346 (mp) REVERT: F 346 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7368 (tm-30) REVERT: F 352 LYS cc_start: 0.7527 (tmtt) cc_final: 0.7037 (tmtt) REVERT: G 95 ASP cc_start: 0.8295 (m-30) cc_final: 0.7954 (t0) REVERT: G 127 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: G 148 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8145 (mttt) REVERT: G 183 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7894 (mt-10) REVERT: G 250 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (tp) REVERT: G 298 GLN cc_start: 0.8063 (mt0) cc_final: 0.7736 (mt0) REVERT: G 331 LYS cc_start: 0.7002 (ptmt) cc_final: 0.6170 (tttm) REVERT: G 344 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (mp) REVERT: G 346 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7369 (tm-30) REVERT: G 352 LYS cc_start: 0.7540 (tmtt) cc_final: 0.7053 (tmtt) REVERT: H 95 ASP cc_start: 0.8295 (m-30) cc_final: 0.7965 (t0) REVERT: H 127 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: H 183 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7889 (mt-10) REVERT: H 250 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8142 (tp) REVERT: H 275 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8592 (mmmt) REVERT: H 298 GLN cc_start: 0.7981 (mt0) cc_final: 0.7602 (mt0) REVERT: H 300 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7814 (tpt90) REVERT: H 331 LYS cc_start: 0.6395 (pttt) cc_final: 0.5511 (tttm) REVERT: H 344 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8338 (mp) REVERT: H 346 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7357 (tm-30) outliers start: 71 outliers final: 17 residues processed: 624 average time/residue: 0.4862 time to fit residues: 427.5551 Evaluate side-chains 596 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 556 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 344 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23912 Z= 0.329 Angle : 0.633 7.726 32304 Z= 0.328 Chirality : 0.045 0.181 3472 Planarity : 0.005 0.041 4248 Dihedral : 4.357 26.928 3259 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.11 % Allowed : 17.12 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2872 helix: 1.53 (0.15), residues: 1112 sheet: 0.17 (0.24), residues: 424 loop : -0.96 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.004 0.001 HIS D 99 PHE 0.020 0.002 PHE H 227 TYR 0.013 0.002 TYR C 207 ARG 0.006 0.001 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 535 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8223 (m-30) cc_final: 0.7932 (t0) REVERT: A 96 ASN cc_start: 0.8188 (m110) cc_final: 0.7876 (m-40) REVERT: A 105 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 116 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 127 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 225 PHE cc_start: 0.8068 (m-10) cc_final: 0.7815 (m-10) REVERT: A 250 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 281 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7600 (ptmm) REVERT: A 298 GLN cc_start: 0.8040 (mt0) cc_final: 0.7684 (mt0) REVERT: A 300 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7857 (tpt90) REVERT: A 331 LYS cc_start: 0.7091 (ptmt) cc_final: 0.6341 (tttm) REVERT: A 344 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 346 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 352 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7095 (tmtt) REVERT: B 96 ASN cc_start: 0.8188 (m110) cc_final: 0.7880 (m-40) REVERT: B 105 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (t) REVERT: B 127 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 183 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 225 PHE cc_start: 0.8045 (m-10) cc_final: 0.7778 (m-80) REVERT: B 250 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 281 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7630 (ptmm) REVERT: B 298 GLN cc_start: 0.7994 (mt0) cc_final: 0.7632 (mt0) REVERT: B 331 LYS cc_start: 0.6925 (ptmt) cc_final: 0.6107 (tttm) REVERT: B 346 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 352 LYS cc_start: 0.7628 (tmtt) cc_final: 0.7168 (tmtt) REVERT: C 96 ASN cc_start: 0.8197 (m110) cc_final: 0.7886 (m-40) REVERT: C 105 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8174 (t) REVERT: C 127 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: C 183 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8015 (mt-10) REVERT: C 211 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: C 225 PHE cc_start: 0.8002 (m-10) cc_final: 0.7705 (m-80) REVERT: C 250 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8191 (tp) REVERT: C 298 GLN cc_start: 0.8005 (mt0) cc_final: 0.7628 (mt0) REVERT: C 331 LYS cc_start: 0.7077 (ptmt) cc_final: 0.6322 (tttm) REVERT: C 344 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 346 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 352 LYS cc_start: 0.7547 (tmtt) cc_final: 0.7102 (tmtt) REVERT: D 96 ASN cc_start: 0.8193 (m110) cc_final: 0.7879 (m-40) REVERT: D 105 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8177 (t) REVERT: D 127 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 148 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7959 (mttt) REVERT: D 211 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: D 225 PHE cc_start: 0.8008 (m-10) cc_final: 0.7726 (m-80) REVERT: D 250 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8201 (tp) REVERT: D 281 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7589 (ptmm) REVERT: D 298 GLN cc_start: 0.8005 (mt0) cc_final: 0.7656 (mt0) REVERT: D 331 LYS cc_start: 0.7006 (ptmt) cc_final: 0.6222 (tttm) REVERT: D 344 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 346 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7424 (tm-30) REVERT: D 352 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7110 (tmtt) REVERT: E 96 ASN cc_start: 0.8187 (m110) cc_final: 0.7876 (m-40) REVERT: E 105 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8164 (t) REVERT: E 127 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: E 183 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7984 (mt-10) REVERT: E 225 PHE cc_start: 0.8017 (m-10) cc_final: 0.7769 (m-80) REVERT: E 250 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8204 (tp) REVERT: E 281 LYS cc_start: 0.7786 (ptmt) cc_final: 0.7575 (ptmm) REVERT: E 298 GLN cc_start: 0.8026 (mt0) cc_final: 0.7675 (mt0) REVERT: E 300 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7871 (tpt90) REVERT: E 331 LYS cc_start: 0.7105 (ptmt) cc_final: 0.6351 (tttm) REVERT: E 346 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 352 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7173 (tmtt) REVERT: F 95 ASP cc_start: 0.8219 (m-30) cc_final: 0.7939 (t0) REVERT: F 96 ASN cc_start: 0.8184 (m110) cc_final: 0.7876 (m-40) REVERT: F 105 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8160 (t) REVERT: F 127 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: F 225 PHE cc_start: 0.7993 (m-10) cc_final: 0.7712 (m-80) REVERT: F 250 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8190 (tp) REVERT: F 281 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7574 (ptmm) REVERT: F 298 GLN cc_start: 0.7993 (mt0) cc_final: 0.7633 (mt0) REVERT: F 331 LYS cc_start: 0.6978 (ptmt) cc_final: 0.5992 (tttm) REVERT: F 346 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7402 (tm-30) REVERT: F 352 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7118 (tmtt) REVERT: G 95 ASP cc_start: 0.8227 (m-30) cc_final: 0.7936 (t0) REVERT: G 96 ASN cc_start: 0.8189 (m110) cc_final: 0.7885 (m-40) REVERT: G 105 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8161 (t) REVERT: G 127 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: G 148 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8065 (mttt) REVERT: G 211 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: G 225 PHE cc_start: 0.8042 (m-10) cc_final: 0.7753 (m-80) REVERT: G 250 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8196 (tp) REVERT: G 281 LYS cc_start: 0.7779 (ptmt) cc_final: 0.7569 (ptmm) REVERT: G 298 GLN cc_start: 0.8004 (mt0) cc_final: 0.7657 (mt0) REVERT: G 331 LYS cc_start: 0.7114 (ptmt) cc_final: 0.6333 (tttm) REVERT: G 346 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7426 (tm-30) REVERT: G 352 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7107 (tmtt) REVERT: H 95 ASP cc_start: 0.8221 (m-30) cc_final: 0.7941 (t0) REVERT: H 96 ASN cc_start: 0.8194 (m110) cc_final: 0.7894 (m-40) REVERT: H 105 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8163 (t) REVERT: H 127 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: H 225 PHE cc_start: 0.7961 (m-10) cc_final: 0.7704 (m-80) REVERT: H 250 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8190 (tp) REVERT: H 281 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7582 (ptmm) REVERT: H 298 GLN cc_start: 0.8002 (mt0) cc_final: 0.7629 (mt0) REVERT: H 331 LYS cc_start: 0.6379 (pttt) cc_final: 0.5496 (tttm) REVERT: H 346 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7385 (tm-30) outliers start: 105 outliers final: 41 residues processed: 591 average time/residue: 0.4518 time to fit residues: 379.4275 Evaluate side-chains 579 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 508 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23912 Z= 0.197 Angle : 0.571 6.855 32304 Z= 0.297 Chirality : 0.042 0.156 3472 Planarity : 0.004 0.040 4248 Dihedral : 4.159 30.203 3259 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.98 % Allowed : 18.73 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2872 helix: 1.69 (0.15), residues: 1112 sheet: -0.15 (0.24), residues: 448 loop : -0.92 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 84 HIS 0.003 0.001 HIS B 99 PHE 0.018 0.002 PHE H 227 TYR 0.008 0.001 TYR C 207 ARG 0.007 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 549 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8259 (m-30) cc_final: 0.7918 (t0) REVERT: A 105 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8036 (t) REVERT: A 116 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 127 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: A 183 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 225 PHE cc_start: 0.7990 (m-10) cc_final: 0.7785 (m-10) REVERT: A 250 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 298 GLN cc_start: 0.8074 (mt0) cc_final: 0.7704 (mt0) REVERT: A 331 LYS cc_start: 0.7234 (ptmt) cc_final: 0.6458 (tttm) REVERT: A 346 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 95 ASP cc_start: 0.8228 (m-30) cc_final: 0.7980 (t0) REVERT: B 105 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 127 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: B 183 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 225 PHE cc_start: 0.7921 (m-10) cc_final: 0.7658 (m-80) REVERT: B 250 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 298 GLN cc_start: 0.8036 (mt0) cc_final: 0.7661 (mt0) REVERT: B 331 LYS cc_start: 0.7023 (ptmt) cc_final: 0.6204 (tttm) REVERT: B 346 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7457 (tm-30) REVERT: C 95 ASP cc_start: 0.8228 (m-30) cc_final: 0.8012 (t0) REVERT: C 105 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8036 (t) REVERT: C 127 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 183 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7940 (mt-10) REVERT: C 211 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: C 225 PHE cc_start: 0.7911 (m-10) cc_final: 0.7642 (m-80) REVERT: C 250 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8187 (tp) REVERT: C 298 GLN cc_start: 0.8046 (mt0) cc_final: 0.7656 (mt0) REVERT: C 331 LYS cc_start: 0.7205 (ptmt) cc_final: 0.6398 (tttm) REVERT: C 344 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 346 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 352 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7033 (tmtt) REVERT: D 95 ASP cc_start: 0.8225 (m-30) cc_final: 0.7993 (t0) REVERT: D 105 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8038 (t) REVERT: D 127 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: D 183 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7915 (mt-10) REVERT: D 211 GLU cc_start: 0.7406 (pm20) cc_final: 0.7173 (pm20) REVERT: D 225 PHE cc_start: 0.7925 (m-10) cc_final: 0.7655 (m-80) REVERT: D 250 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8189 (tp) REVERT: D 275 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8443 (mmmt) REVERT: D 298 GLN cc_start: 0.8050 (mt0) cc_final: 0.7688 (mt0) REVERT: D 331 LYS cc_start: 0.7134 (ptmt) cc_final: 0.6409 (tttm) REVERT: D 344 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8349 (mp) REVERT: D 346 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 352 LYS cc_start: 0.7528 (tmtt) cc_final: 0.7044 (tmtt) REVERT: E 127 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: E 183 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 225 PHE cc_start: 0.7901 (m-10) cc_final: 0.7640 (m-80) REVERT: E 250 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8184 (tp) REVERT: E 298 GLN cc_start: 0.8003 (mt0) cc_final: 0.7642 (mt0) REVERT: E 300 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7826 (tpt90) REVERT: E 331 LYS cc_start: 0.7259 (ptmt) cc_final: 0.6466 (tttm) REVERT: E 346 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7429 (tm-30) REVERT: F 95 ASP cc_start: 0.8181 (m-30) cc_final: 0.7858 (t0) REVERT: F 127 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: F 225 PHE cc_start: 0.7915 (m-10) cc_final: 0.7649 (m-80) REVERT: F 250 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8172 (tp) REVERT: F 298 GLN cc_start: 0.8035 (mt0) cc_final: 0.7658 (mt0) REVERT: F 331 LYS cc_start: 0.7003 (ptmt) cc_final: 0.6026 (tttm) REVERT: F 346 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7419 (tm-30) REVERT: G 95 ASP cc_start: 0.8265 (m-30) cc_final: 0.7908 (t0) REVERT: G 105 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8045 (t) REVERT: G 127 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: G 148 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8063 (mttt) REVERT: G 183 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7931 (mt-10) REVERT: G 211 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: G 225 PHE cc_start: 0.7876 (m-10) cc_final: 0.7641 (m-80) REVERT: G 275 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8451 (mmmt) REVERT: G 298 GLN cc_start: 0.7975 (mt0) cc_final: 0.7622 (mt0) REVERT: G 331 LYS cc_start: 0.7174 (ptmt) cc_final: 0.6290 (tttm) REVERT: G 346 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7420 (tm-30) REVERT: G 352 LYS cc_start: 0.7621 (tmtt) cc_final: 0.7130 (tmtt) REVERT: H 95 ASP cc_start: 0.8268 (m-30) cc_final: 0.7918 (t0) REVERT: H 127 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: H 183 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7934 (mt-10) REVERT: H 225 PHE cc_start: 0.7916 (m-10) cc_final: 0.7625 (m-80) REVERT: H 250 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8175 (tp) REVERT: H 298 GLN cc_start: 0.8043 (mt0) cc_final: 0.7653 (mt0) REVERT: H 331 LYS cc_start: 0.6398 (pttt) cc_final: 0.5502 (tttp) REVERT: H 346 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 76 outliers final: 33 residues processed: 593 average time/residue: 0.4386 time to fit residues: 374.5648 Evaluate side-chains 543 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 486 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 280 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 169 optimal weight: 0.0670 chunk 128 optimal weight: 4.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23912 Z= 0.332 Angle : 0.641 8.382 32304 Z= 0.330 Chirality : 0.045 0.183 3472 Planarity : 0.005 0.046 4248 Dihedral : 4.362 17.303 3258 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.45 % Allowed : 19.04 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2872 helix: 1.42 (0.15), residues: 1112 sheet: 0.06 (0.24), residues: 424 loop : -1.04 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 84 HIS 0.004 0.001 HIS B 99 PHE 0.020 0.002 PHE C 227 TYR 0.013 0.002 TYR C 207 ARG 0.009 0.001 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 520 time to evaluate : 2.995 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: A 95 ASP cc_start: 0.8241 (m-30) cc_final: 0.7922 (t0) REVERT: A 96 ASN cc_start: 0.8312 (m-40) cc_final: 0.7936 (m-40) REVERT: A 105 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8138 (t) REVERT: A 116 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 127 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 298 GLN cc_start: 0.8016 (mt0) cc_final: 0.7660 (mt0) REVERT: A 331 LYS cc_start: 0.7155 (ptmt) cc_final: 0.6369 (tttm) REVERT: A 346 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 95 ASP cc_start: 0.8302 (m-30) cc_final: 0.8048 (t0) REVERT: B 96 ASN cc_start: 0.8315 (m-40) cc_final: 0.8004 (m-40) REVERT: B 105 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 127 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: B 183 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 225 PHE cc_start: 0.7924 (m-10) cc_final: 0.7648 (m-80) REVERT: B 250 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8188 (tp) REVERT: B 298 GLN cc_start: 0.8051 (mt0) cc_final: 0.7675 (mt0) REVERT: B 331 LYS cc_start: 0.6939 (ptmt) cc_final: 0.6127 (tttm) REVERT: B 346 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 95 ASP cc_start: 0.8217 (m-30) cc_final: 0.7991 (t0) REVERT: C 105 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8163 (t) REVERT: C 127 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: C 183 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7976 (mt-10) REVERT: C 225 PHE cc_start: 0.7913 (m-10) cc_final: 0.7652 (m-80) REVERT: C 250 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 298 GLN cc_start: 0.7981 (mt0) cc_final: 0.7606 (mt0) REVERT: C 331 LYS cc_start: 0.7190 (ptmt) cc_final: 0.6355 (tttm) REVERT: C 346 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 352 LYS cc_start: 0.7539 (tmtt) cc_final: 0.7083 (tmtt) REVERT: D 95 ASP cc_start: 0.8214 (m-30) cc_final: 0.7984 (t0) REVERT: D 105 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (t) REVERT: D 127 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: D 183 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 225 PHE cc_start: 0.7935 (m-10) cc_final: 0.7651 (m-80) REVERT: D 250 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8198 (tp) REVERT: D 298 GLN cc_start: 0.7983 (mt0) cc_final: 0.7634 (mt0) REVERT: D 331 LYS cc_start: 0.7106 (ptmt) cc_final: 0.6340 (tttm) REVERT: D 346 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7418 (tm-30) REVERT: E 105 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8145 (t) REVERT: E 127 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: E 225 PHE cc_start: 0.7910 (m-10) cc_final: 0.7644 (m-80) REVERT: E 250 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8208 (tp) REVERT: E 298 GLN cc_start: 0.8022 (mt0) cc_final: 0.7666 (mt0) REVERT: E 331 LYS cc_start: 0.7249 (ptmt) cc_final: 0.6432 (tttm) REVERT: E 346 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 352 LYS cc_start: 0.7735 (tmtt) cc_final: 0.7469 (tmtt) REVERT: F 95 ASP cc_start: 0.8232 (m-30) cc_final: 0.7942 (t0) REVERT: F 96 ASN cc_start: 0.8329 (m-40) cc_final: 0.8011 (m-40) REVERT: F 105 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8168 (t) REVERT: F 127 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: F 225 PHE cc_start: 0.8001 (m-10) cc_final: 0.7723 (m-80) REVERT: F 298 GLN cc_start: 0.7967 (mt0) cc_final: 0.7611 (mt0) REVERT: F 331 LYS cc_start: 0.7033 (ptmt) cc_final: 0.6046 (tttp) REVERT: F 346 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 352 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7450 (tmtt) REVERT: G 95 ASP cc_start: 0.8240 (m-30) cc_final: 0.7935 (t0) REVERT: G 96 ASN cc_start: 0.8319 (m-40) cc_final: 0.7953 (m-40) REVERT: G 105 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (t) REVERT: G 127 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: G 225 PHE cc_start: 0.7995 (m-10) cc_final: 0.7725 (m-80) REVERT: G 275 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8482 (mmmt) REVERT: G 298 GLN cc_start: 0.7982 (mt0) cc_final: 0.7640 (mt0) REVERT: G 331 LYS cc_start: 0.7199 (ptmt) cc_final: 0.6305 (tttm) REVERT: G 346 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7421 (tm-30) REVERT: G 352 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7183 (tmtt) REVERT: H 95 ASP cc_start: 0.8238 (m-30) cc_final: 0.7946 (t0) REVERT: H 96 ASN cc_start: 0.8321 (m-40) cc_final: 0.7952 (m-40) REVERT: H 105 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8161 (t) REVERT: H 127 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: H 183 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7987 (mt-10) REVERT: H 225 PHE cc_start: 0.7895 (m-10) cc_final: 0.7616 (m-80) REVERT: H 250 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8186 (tp) REVERT: H 298 GLN cc_start: 0.7978 (mt0) cc_final: 0.7602 (mt0) REVERT: H 331 LYS cc_start: 0.6402 (pttt) cc_final: 0.5538 (tttm) REVERT: H 346 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7418 (tm-30) REVERT: H 352 LYS cc_start: 0.7715 (tmtt) cc_final: 0.6907 (tptp) outliers start: 88 outliers final: 45 residues processed: 575 average time/residue: 0.4427 time to fit residues: 369.0834 Evaluate side-chains 545 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 479 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 176 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23912 Z= 0.187 Angle : 0.597 7.305 32304 Z= 0.307 Chirality : 0.043 0.207 3472 Planarity : 0.005 0.046 4248 Dihedral : 4.132 16.035 3258 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.35 % Allowed : 19.91 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2872 helix: 1.60 (0.15), residues: 1112 sheet: -0.19 (0.23), residues: 448 loop : -0.95 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 84 HIS 0.003 0.001 HIS G 99 PHE 0.021 0.002 PHE A 227 TYR 0.008 0.001 TYR G 207 ARG 0.008 0.000 ARG G 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 529 time to evaluate : 2.844 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: A 95 ASP cc_start: 0.8235 (m-30) cc_final: 0.7911 (t0) REVERT: A 96 ASN cc_start: 0.8175 (m-40) cc_final: 0.7919 (m-40) REVERT: A 105 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (t) REVERT: A 116 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 127 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: A 183 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 298 GLN cc_start: 0.8067 (mt0) cc_final: 0.7704 (mt0) REVERT: A 331 LYS cc_start: 0.7251 (ptmt) cc_final: 0.6423 (tttm) REVERT: A 346 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 95 ASP cc_start: 0.8312 (m-30) cc_final: 0.8027 (t0) REVERT: B 96 ASN cc_start: 0.8231 (m-40) cc_final: 0.7981 (m-40) REVERT: B 105 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7977 (t) REVERT: B 127 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: B 183 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 225 PHE cc_start: 0.7871 (m-10) cc_final: 0.7614 (m-80) REVERT: B 298 GLN cc_start: 0.8013 (mt0) cc_final: 0.7648 (mt0) REVERT: B 331 LYS cc_start: 0.7099 (ptmt) cc_final: 0.6167 (tttm) REVERT: B 346 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 352 LYS cc_start: 0.7757 (tmtt) cc_final: 0.7466 (tmtt) REVERT: C 95 ASP cc_start: 0.8314 (m-30) cc_final: 0.8014 (t0) REVERT: C 96 ASN cc_start: 0.8234 (m-40) cc_final: 0.7868 (m-40) REVERT: C 105 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8029 (t) REVERT: C 127 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: C 183 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 225 PHE cc_start: 0.7855 (m-10) cc_final: 0.7601 (m-80) REVERT: C 250 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8165 (tp) REVERT: C 298 GLN cc_start: 0.8029 (mt0) cc_final: 0.7648 (mt0) REVERT: C 331 LYS cc_start: 0.7218 (ptmt) cc_final: 0.6785 (ptmm) REVERT: C 346 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7457 (tm-30) REVERT: C 352 LYS cc_start: 0.7598 (tmtt) cc_final: 0.7121 (tmtt) REVERT: D 95 ASP cc_start: 0.8308 (m-30) cc_final: 0.8002 (t0) REVERT: D 96 ASN cc_start: 0.8233 (m-40) cc_final: 0.7869 (m-40) REVERT: D 105 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7975 (t) REVERT: D 127 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: D 183 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 225 PHE cc_start: 0.7847 (m-10) cc_final: 0.7624 (m-80) REVERT: D 250 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (tp) REVERT: D 298 GLN cc_start: 0.8032 (mt0) cc_final: 0.7681 (mt0) REVERT: D 331 LYS cc_start: 0.7202 (ptmt) cc_final: 0.6368 (tttp) REVERT: D 346 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7468 (tm-30) REVERT: E 96 ASN cc_start: 0.8181 (m-40) cc_final: 0.7942 (m-40) REVERT: E 105 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8021 (t) REVERT: E 127 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: E 183 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 225 PHE cc_start: 0.7827 (m-10) cc_final: 0.7601 (m-80) REVERT: E 250 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8180 (tp) REVERT: E 298 GLN cc_start: 0.8058 (mt0) cc_final: 0.7719 (mt0) REVERT: E 331 LYS cc_start: 0.7228 (ptmt) cc_final: 0.6428 (tttm) REVERT: E 346 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 95 ASP cc_start: 0.8241 (m-30) cc_final: 0.7896 (t0) REVERT: F 96 ASN cc_start: 0.8239 (m-40) cc_final: 0.7976 (m-40) REVERT: F 105 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8040 (t) REVERT: F 127 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: F 225 PHE cc_start: 0.7870 (m-10) cc_final: 0.7645 (m-80) REVERT: F 298 GLN cc_start: 0.8012 (mt0) cc_final: 0.7646 (mt0) REVERT: F 331 LYS cc_start: 0.7177 (ptmt) cc_final: 0.6191 (tttm) REVERT: F 346 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7378 (tm-30) REVERT: G 95 ASP cc_start: 0.8249 (m-30) cc_final: 0.7892 (t0) REVERT: G 96 ASN cc_start: 0.8184 (m-40) cc_final: 0.7934 (m-40) REVERT: G 105 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8019 (t) REVERT: G 127 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: G 183 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7921 (mt-10) REVERT: G 225 PHE cc_start: 0.7842 (m-10) cc_final: 0.7619 (m-80) REVERT: G 298 GLN cc_start: 0.8033 (mt0) cc_final: 0.7681 (mt0) REVERT: G 331 LYS cc_start: 0.7239 (ptmt) cc_final: 0.6311 (tttm) REVERT: G 346 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7479 (tm-30) REVERT: H 95 ASP cc_start: 0.8258 (m-30) cc_final: 0.7906 (t0) REVERT: H 96 ASN cc_start: 0.8179 (m-40) cc_final: 0.7925 (m-40) REVERT: H 105 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8026 (t) REVERT: H 127 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: H 183 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7909 (mt-10) REVERT: H 225 PHE cc_start: 0.7861 (m-10) cc_final: 0.7619 (m-80) REVERT: H 298 GLN cc_start: 0.8024 (mt0) cc_final: 0.7641 (mt0) REVERT: H 331 LYS cc_start: 0.6414 (pttt) cc_final: 0.5492 (tttm) REVERT: H 346 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 60 outliers final: 29 residues processed: 569 average time/residue: 0.4325 time to fit residues: 355.7866 Evaluate side-chains 547 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 499 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 242 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23912 Z= 0.205 Angle : 0.622 7.745 32304 Z= 0.318 Chirality : 0.043 0.186 3472 Planarity : 0.005 0.042 4248 Dihedral : 4.113 15.797 3258 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.23 % Allowed : 20.45 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 2872 helix: 1.63 (0.15), residues: 1112 sheet: -0.20 (0.24), residues: 448 loop : -0.94 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 261 HIS 0.003 0.001 HIS G 99 PHE 0.021 0.002 PHE C 227 TYR 0.011 0.001 TYR H 207 ARG 0.008 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 504 time to evaluate : 2.555 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: A 95 ASP cc_start: 0.8265 (m-30) cc_final: 0.7900 (t0) REVERT: A 96 ASN cc_start: 0.8192 (m-40) cc_final: 0.7961 (m-40) REVERT: A 105 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8007 (t) REVERT: A 113 GLU cc_start: 0.8526 (mp0) cc_final: 0.8220 (mp0) REVERT: A 116 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 127 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: A 183 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 298 GLN cc_start: 0.8062 (mt0) cc_final: 0.7700 (mt0) REVERT: A 331 LYS cc_start: 0.7188 (ptmt) cc_final: 0.6361 (tttm) REVERT: A 346 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 352 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7416 (tmtt) REVERT: B 95 ASP cc_start: 0.8350 (m-30) cc_final: 0.8028 (t0) REVERT: B 96 ASN cc_start: 0.8181 (m-40) cc_final: 0.7960 (m-40) REVERT: B 105 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7995 (t) REVERT: B 127 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 183 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 225 PHE cc_start: 0.7851 (m-10) cc_final: 0.7620 (m-80) REVERT: B 298 GLN cc_start: 0.8012 (mt0) cc_final: 0.7636 (mt0) REVERT: B 346 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 352 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7477 (tmtt) REVERT: C 95 ASP cc_start: 0.8348 (m-30) cc_final: 0.8016 (t0) REVERT: C 96 ASN cc_start: 0.8184 (m-40) cc_final: 0.7901 (m-40) REVERT: C 105 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8001 (t) REVERT: C 127 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: C 183 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 225 PHE cc_start: 0.7847 (m-10) cc_final: 0.7614 (m-80) REVERT: C 298 GLN cc_start: 0.8031 (mt0) cc_final: 0.7641 (mt0) REVERT: C 331 LYS cc_start: 0.7222 (ptmt) cc_final: 0.6397 (tttp) REVERT: C 346 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 352 LYS cc_start: 0.7597 (tmtt) cc_final: 0.7132 (tmtt) REVERT: D 95 ASP cc_start: 0.8324 (m-30) cc_final: 0.8006 (t0) REVERT: D 96 ASN cc_start: 0.8184 (m-40) cc_final: 0.7900 (m-40) REVERT: D 105 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8010 (t) REVERT: D 127 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: D 183 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 225 PHE cc_start: 0.7861 (m-10) cc_final: 0.7603 (m-80) REVERT: D 250 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8184 (tp) REVERT: D 298 GLN cc_start: 0.8035 (mt0) cc_final: 0.7685 (mt0) REVERT: D 331 LYS cc_start: 0.7028 (ptmt) cc_final: 0.6169 (tttp) REVERT: D 346 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 352 LYS cc_start: 0.7716 (tmtt) cc_final: 0.6856 (tptp) REVERT: E 105 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8035 (t) REVERT: E 127 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: E 183 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 225 PHE cc_start: 0.7809 (m-10) cc_final: 0.7586 (m-80) REVERT: E 298 GLN cc_start: 0.8052 (mt0) cc_final: 0.7695 (mt0) REVERT: E 331 LYS cc_start: 0.7230 (ptmt) cc_final: 0.6431 (tttm) REVERT: E 346 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7401 (tm-30) REVERT: E 352 LYS cc_start: 0.7794 (tmtt) cc_final: 0.6880 (tptp) REVERT: F 95 ASP cc_start: 0.8265 (m-30) cc_final: 0.7899 (t0) REVERT: F 96 ASN cc_start: 0.8191 (m-40) cc_final: 0.7962 (m-40) REVERT: F 105 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (t) REVERT: F 127 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: F 225 PHE cc_start: 0.7875 (m-10) cc_final: 0.7628 (m-80) REVERT: F 298 GLN cc_start: 0.8010 (mt0) cc_final: 0.7648 (mt0) REVERT: F 331 LYS cc_start: 0.7180 (ptmt) cc_final: 0.6174 (tttp) REVERT: F 346 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7400 (tm-30) REVERT: F 352 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7494 (tmtt) REVERT: G 95 ASP cc_start: 0.8266 (m-30) cc_final: 0.7886 (t0) REVERT: G 96 ASN cc_start: 0.8196 (m-40) cc_final: 0.7973 (m-40) REVERT: G 105 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8053 (t) REVERT: G 127 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: G 183 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7910 (mt-10) REVERT: G 225 PHE cc_start: 0.7841 (m-10) cc_final: 0.7611 (m-80) REVERT: G 298 GLN cc_start: 0.8035 (mt0) cc_final: 0.7683 (mt0) REVERT: G 331 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6297 (tttp) REVERT: G 346 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7494 (tm-30) REVERT: G 352 LYS cc_start: 0.7897 (tmtt) cc_final: 0.6978 (tptp) REVERT: H 95 ASP cc_start: 0.8277 (m-30) cc_final: 0.7898 (t0) REVERT: H 96 ASN cc_start: 0.8188 (m-40) cc_final: 0.7957 (m-40) REVERT: H 105 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8033 (t) REVERT: H 127 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: H 183 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7919 (mt-10) REVERT: H 225 PHE cc_start: 0.7859 (m-10) cc_final: 0.7622 (m-80) REVERT: H 298 GLN cc_start: 0.8019 (mt0) cc_final: 0.7631 (mt0) REVERT: H 331 LYS cc_start: 0.6431 (pttt) cc_final: 0.5496 (tttp) REVERT: H 346 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 352 LYS cc_start: 0.7789 (tmtt) cc_final: 0.7039 (tptp) outliers start: 57 outliers final: 32 residues processed: 541 average time/residue: 0.4116 time to fit residues: 326.0288 Evaluate side-chains 551 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 502 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23912 Z= 0.229 Angle : 0.635 9.021 32304 Z= 0.324 Chirality : 0.044 0.210 3472 Planarity : 0.005 0.041 4248 Dihedral : 4.115 15.969 3258 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.19 % Allowed : 20.49 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2872 helix: 1.60 (0.15), residues: 1112 sheet: -0.28 (0.23), residues: 448 loop : -0.97 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS H 99 PHE 0.021 0.002 PHE C 227 TYR 0.012 0.001 TYR G 207 ARG 0.008 0.000 ARG G 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 520 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8274 (m-30) cc_final: 0.7910 (t0) REVERT: A 96 ASN cc_start: 0.8229 (m-40) cc_final: 0.7989 (m-40) REVERT: A 105 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 116 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 127 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: A 183 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 251 TRP cc_start: 0.8478 (t60) cc_final: 0.8132 (t60) REVERT: A 298 GLN cc_start: 0.8059 (mt0) cc_final: 0.7675 (mt0) REVERT: A 331 LYS cc_start: 0.7138 (ptmt) cc_final: 0.6338 (tttp) REVERT: A 346 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 95 ASP cc_start: 0.8358 (m-30) cc_final: 0.8041 (t0) REVERT: B 96 ASN cc_start: 0.8268 (m-40) cc_final: 0.8021 (m-40) REVERT: B 105 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7998 (t) REVERT: B 127 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 183 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 225 PHE cc_start: 0.7862 (m-10) cc_final: 0.7593 (m-80) REVERT: B 298 GLN cc_start: 0.8014 (mt0) cc_final: 0.7623 (mt0) REVERT: B 346 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 352 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7411 (tmtt) REVERT: C 95 ASP cc_start: 0.8333 (m-30) cc_final: 0.8015 (t0) REVERT: C 96 ASN cc_start: 0.8210 (m-40) cc_final: 0.7894 (m-40) REVERT: C 105 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8029 (t) REVERT: C 127 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: C 183 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 225 PHE cc_start: 0.7870 (m-10) cc_final: 0.7620 (m-80) REVERT: C 251 TRP cc_start: 0.8429 (t60) cc_final: 0.8062 (t60) REVERT: C 298 GLN cc_start: 0.8021 (mt0) cc_final: 0.7636 (mt0) REVERT: C 331 LYS cc_start: 0.7226 (ptmt) cc_final: 0.6433 (tttm) REVERT: C 346 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 352 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7137 (tmtt) REVERT: D 95 ASP cc_start: 0.8330 (m-30) cc_final: 0.8006 (t0) REVERT: D 96 ASN cc_start: 0.8194 (m-40) cc_final: 0.7910 (m-40) REVERT: D 105 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8043 (t) REVERT: D 127 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: D 183 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 225 PHE cc_start: 0.7853 (m-10) cc_final: 0.7624 (m-80) REVERT: D 250 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8199 (tp) REVERT: D 251 TRP cc_start: 0.8396 (t60) cc_final: 0.8033 (t60) REVERT: D 298 GLN cc_start: 0.8035 (mt0) cc_final: 0.7684 (mt0) REVERT: D 331 LYS cc_start: 0.7026 (ptmt) cc_final: 0.6158 (tttm) REVERT: D 346 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 105 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8069 (t) REVERT: E 113 GLU cc_start: 0.8509 (mp0) cc_final: 0.8309 (mp0) REVERT: E 127 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: E 183 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7957 (mt-10) REVERT: E 225 PHE cc_start: 0.7808 (m-10) cc_final: 0.7581 (m-80) REVERT: E 251 TRP cc_start: 0.8430 (t60) cc_final: 0.8066 (t60) REVERT: E 298 GLN cc_start: 0.8049 (mt0) cc_final: 0.7693 (mt0) REVERT: E 331 LYS cc_start: 0.7148 (ptmt) cc_final: 0.6348 (tttm) REVERT: E 346 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 352 LYS cc_start: 0.7781 (tmtt) cc_final: 0.6839 (tptp) REVERT: F 95 ASP cc_start: 0.8272 (m-30) cc_final: 0.7905 (t0) REVERT: F 96 ASN cc_start: 0.8284 (m-40) cc_final: 0.8031 (m-40) REVERT: F 105 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8103 (t) REVERT: F 127 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: F 225 PHE cc_start: 0.7889 (m-10) cc_final: 0.7632 (m-80) REVERT: F 298 GLN cc_start: 0.8013 (mt0) cc_final: 0.7643 (mt0) REVERT: F 331 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6168 (tttm) REVERT: F 346 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7398 (tm-30) REVERT: F 352 LYS cc_start: 0.7783 (tmtt) cc_final: 0.7497 (tmtt) REVERT: G 95 ASP cc_start: 0.8280 (m-30) cc_final: 0.7894 (t0) REVERT: G 96 ASN cc_start: 0.8228 (m-40) cc_final: 0.7989 (m-40) REVERT: G 105 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8072 (t) REVERT: G 113 GLU cc_start: 0.8521 (mp0) cc_final: 0.8310 (mp0) REVERT: G 127 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: G 183 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7917 (mt-10) REVERT: G 225 PHE cc_start: 0.7877 (m-10) cc_final: 0.7545 (m-80) REVERT: G 261 TRP cc_start: 0.8502 (m-10) cc_final: 0.8004 (m-10) REVERT: G 298 GLN cc_start: 0.8038 (mt0) cc_final: 0.7692 (mt0) REVERT: G 331 LYS cc_start: 0.7218 (ptmt) cc_final: 0.6302 (tttp) REVERT: G 346 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7499 (tm-30) REVERT: G 352 LYS cc_start: 0.7809 (tmtt) cc_final: 0.7454 (tmtt) REVERT: H 95 ASP cc_start: 0.8287 (m-30) cc_final: 0.7912 (t0) REVERT: H 96 ASN cc_start: 0.8223 (m-40) cc_final: 0.7976 (m-40) REVERT: H 105 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8082 (t) REVERT: H 113 GLU cc_start: 0.8530 (mp0) cc_final: 0.8329 (mp0) REVERT: H 127 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: H 183 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7920 (mt-10) REVERT: H 225 PHE cc_start: 0.7875 (m-10) cc_final: 0.7627 (m-80) REVERT: H 251 TRP cc_start: 0.8414 (t60) cc_final: 0.8062 (t60) REVERT: H 298 GLN cc_start: 0.8020 (mt0) cc_final: 0.7630 (mt0) REVERT: H 346 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 352 LYS cc_start: 0.7811 (tmtt) cc_final: 0.7047 (tptp) outliers start: 56 outliers final: 32 residues processed: 555 average time/residue: 0.4138 time to fit residues: 335.0378 Evaluate side-chains 556 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 507 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138500 restraints weight = 29690.106| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.97 r_work: 0.3391 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23912 Z= 0.205 Angle : 0.633 7.976 32304 Z= 0.323 Chirality : 0.044 0.178 3472 Planarity : 0.005 0.047 4248 Dihedral : 4.068 15.670 3258 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.08 % Allowed : 20.89 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2872 helix: 1.66 (0.15), residues: 1112 sheet: -0.25 (0.24), residues: 448 loop : -0.93 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 251 HIS 0.003 0.001 HIS H 99 PHE 0.021 0.002 PHE A 227 TYR 0.012 0.001 TYR C 207 ARG 0.008 0.000 ARG H 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6577.93 seconds wall clock time: 118 minutes 31.31 seconds (7111.31 seconds total)