Starting phenix.real_space_refine on Fri Jul 26 04:21:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/07_2024/7pbs_13301_neut_trim.cif" } resolution = 3.3 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= 0.003 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: 7 Type Number sf(0) Gaussians P 47 5.49 5 Mg 5 5.21 5 S 102 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3152 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31328 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.72, per 1000 atoms: 0.47 Number of scatterers: 31328 At special positions: 0 Unit cell: (123.2, 137.5, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 102 16.00 P 47 15.00 Mg 5 11.99 O 3152 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 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: 22.72 Conformation dependent library (CDL) restraints added in 3.0 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 21 sheets defined 60.1% alpha, 11.4% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 13.40 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.617A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.559A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.654A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.413A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.590A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.612A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.783A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.585A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.522A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.605A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.565A pdb=" N MET B 115 " --> pdb=" O ILE B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.524A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.515A pdb=" N TYR B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.505A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.539A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 129 removed outlier: 4.137A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.519A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.787A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.691A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.780A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.720A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.435A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.593A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.667A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.578A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 234 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.575A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.512A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.557A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.532A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.544A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.658A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.743A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.816A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.736A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 removed outlier: 3.746A pdb=" N ASN E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.712A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 100 removed outlier: 3.713A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.483A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.542A pdb=" N PHE F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 213 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.528A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 56 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.008A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.408A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.349A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.441A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.340A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.189A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.507A pdb=" N LYS F 81 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP F 110 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR F 83 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC2, first strand: chain 'F' and resid 200 through 201 removed outlier: 7.085A pdb=" N THR F 200 " --> pdb=" O ILE F 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 308 through 311 775 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 11.13 Time building geometry restraints manager: 24.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15439 1.05 - 1.28: 2655 1.28 - 1.50: 6782 1.50 - 1.72: 6592 1.72 - 1.94: 199 Bond restraints: 31667 Sorted by residual: bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31662 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.07: 940 107.07 - 114.32: 38556 114.32 - 121.57: 12164 121.57 - 128.83: 5569 128.83 - 136.08: 92 Bond angle restraints: 57321 Sorted by residual: angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.48 104.85 5.63 1.48e+00 4.57e-01 1.45e+01 angle pdb=" N ILE E 233 " pdb=" CA ILE E 233 " pdb=" C ILE E 233 " ideal model delta sigma weight residual 111.62 108.75 2.87 7.90e-01 1.60e+00 1.32e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.22 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 118.12 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N LEU D 251 " pdb=" CA LEU D 251 " pdb=" C LEU D 251 " ideal model delta sigma weight residual 110.20 105.10 5.10 1.58e+00 4.01e-01 1.04e+01 ... (remaining 57316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 14162 34.75 - 69.50: 515 69.50 - 104.25: 16 104.25 - 139.00: 3 139.00 - 173.75: 3 Dihedral angle restraints: 14699 sinusoidal: 8430 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.10 -157.10 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O1A AGS F 401 " pdb=" O3A AGS F 401 " pdb=" PA AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sinusoidal sigma weight residual -67.73 106.02 -173.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 76.82 -144.55 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 14696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2269 0.083 - 0.166: 228 0.166 - 0.248: 0 0.248 - 0.331: 0 0.331 - 0.414: 1 Chirality restraints: 2498 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" C3' DA U 10 " pdb=" C4' DA U 10 " pdb=" O3' DA U 10 " pdb=" C2' DA U 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 2495 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.145 9.50e-02 1.11e+02 6.91e-02 5.71e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.099 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.312 9.50e-02 1.11e+02 1.13e-01 5.48e+01 pdb=" NE ARG E 160 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.168 9.50e-02 1.11e+02 7.21e-02 4.99e+01 pdb=" NE ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.083 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.084 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 760 2.13 - 2.75: 56501 2.75 - 3.37: 84017 3.37 - 3.98: 108550 3.98 - 4.60: 175860 Nonbonded interactions: 425688 Sorted by model distance: nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.516 1.850 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.525 1.850 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.534 1.850 nonbonded pdb=" HZ3 LYS D 46 " pdb=" O GLU D 75 " model vdw 1.538 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.568 1.850 ... (remaining 425683 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' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 2.380 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: 0.460 Extract box with map and model: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 103.970 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.005 0.041 16228 Z= 0.336 Angle : 0.715 10.783 22105 Z= 0.415 Chirality : 0.046 0.414 2498 Planarity : 0.011 0.137 2739 Dihedral : 14.970 173.751 6287 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.25 % Allowed : 1.37 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 1902 helix: -0.48 (0.15), residues: 1018 sheet: 0.80 (0.30), residues: 309 loop : 0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS B 113 PHE 0.020 0.003 PHE A 25 TYR 0.025 0.005 TYR E 273 ARG 0.025 0.003 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 420 time to evaluate : 2.351 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 33 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7429 (mttt) REVERT: A 43 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 131 TYR cc_start: 0.8742 (p90) cc_final: 0.7984 (p90) REVERT: A 160 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7770 (ptp-170) REVERT: A 234 MET cc_start: 0.7411 (ptp) cc_final: 0.7067 (ptp) REVERT: A 252 ASP cc_start: 0.7867 (t0) cc_final: 0.7416 (t0) REVERT: A 282 THR cc_start: 0.8514 (m) cc_final: 0.8032 (p) REVERT: A 292 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6968 (tt0) REVERT: A 309 MET cc_start: 0.7326 (ttm) cc_final: 0.7123 (ttt) REVERT: A 325 MET cc_start: 0.7672 (mmm) cc_final: 0.7248 (mmt) REVERT: B 49 ASP cc_start: 0.7720 (t0) cc_final: 0.7440 (t0) REVERT: B 102 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6945 (mt-10) REVERT: B 178 MET cc_start: 0.8658 (mmm) cc_final: 0.7603 (mmt) REVERT: B 199 MET cc_start: 0.7852 (mmp) cc_final: 0.7277 (tpt) REVERT: B 234 MET cc_start: 0.8342 (mmp) cc_final: 0.8123 (mmm) REVERT: C 47 LEU cc_start: 0.8037 (tp) cc_final: 0.7701 (mt) REVERT: C 260 TYR cc_start: 0.7683 (t80) cc_final: 0.7360 (t80) REVERT: D 78 VAL cc_start: 0.7517 (t) cc_final: 0.7270 (p) REVERT: D 264 LYS cc_start: 0.7838 (tttt) cc_final: 0.7482 (ttpt) REVERT: D 292 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7162 (mp0) REVERT: D 309 MET cc_start: 0.7813 (mtp) cc_final: 0.7580 (mtp) REVERT: D 330 THR cc_start: 0.6052 (m) cc_final: 0.5665 (p) REVERT: E 76 MET cc_start: 0.8489 (mmm) cc_final: 0.7796 (mmt) REVERT: E 89 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6159 (mm-30) REVERT: E 98 LEU cc_start: 0.8658 (mt) cc_final: 0.8372 (mm) REVERT: E 111 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7733 (mt-10) REVERT: E 125 SER cc_start: 0.7697 (m) cc_final: 0.7490 (t) REVERT: E 143 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6011 (mtm110) REVERT: E 179 GLU cc_start: 0.7682 (pt0) cc_final: 0.7456 (pt0) REVERT: E 242 LYS cc_start: 0.7315 (pttm) cc_final: 0.6655 (tppt) REVERT: E 267 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6663 (ttp-110) REVERT: E 299 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6126 (mt-10) REVERT: E 301 TYR cc_start: 0.7101 (t80) cc_final: 0.6825 (t80) REVERT: F 102 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6766 (mp0) REVERT: F 125 SER cc_start: 0.8456 (m) cc_final: 0.8213 (p) REVERT: F 143 ARG cc_start: 0.7562 (ptt90) cc_final: 0.7229 (ptt-90) REVERT: F 144 SER cc_start: 0.8630 (p) cc_final: 0.8349 (t) REVERT: F 199 MET cc_start: 0.7222 (tpp) cc_final: 0.6662 (tpp) REVERT: F 267 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5891 (ttp80) REVERT: F 286 ASN cc_start: 0.7162 (m-40) cc_final: 0.6901 (m110) outliers start: 4 outliers final: 1 residues processed: 421 average time/residue: 0.7477 time to fit residues: 438.9159 Evaluate side-chains 277 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 232 GLN D 286 ASN E 74 ASN E 166 ASN F 23 GLN F 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16228 Z= 0.248 Angle : 0.602 7.551 22105 Z= 0.331 Chirality : 0.042 0.159 2498 Planarity : 0.005 0.064 2739 Dihedral : 15.201 172.094 2563 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.94 % Allowed : 5.99 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.68 (0.19), residues: 1902 helix: 0.48 (0.16), residues: 1048 sheet: 1.27 (0.31), residues: 280 loop : 0.27 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 54 PHE 0.008 0.001 PHE B 25 TYR 0.009 0.001 TYR C 260 ARG 0.005 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 270 time to evaluate : 2.826 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 131 TYR cc_start: 0.8800 (p90) cc_final: 0.8223 (p90) REVERT: A 234 MET cc_start: 0.7579 (ptp) cc_final: 0.7139 (ptp) REVERT: A 252 ASP cc_start: 0.7651 (t0) cc_final: 0.7036 (t0) REVERT: A 282 THR cc_start: 0.7995 (m) cc_final: 0.7726 (p) REVERT: A 309 MET cc_start: 0.7283 (ttm) cc_final: 0.7059 (ttt) REVERT: A 325 MET cc_start: 0.7677 (mmm) cc_final: 0.7280 (mmt) REVERT: B 102 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6979 (mt-10) REVERT: B 199 MET cc_start: 0.7995 (mmp) cc_final: 0.7258 (tpt) REVERT: B 234 MET cc_start: 0.8295 (mmp) cc_final: 0.8026 (mmt) REVERT: B 296 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7494 (t0) REVERT: C 178 MET cc_start: 0.8721 (mmt) cc_final: 0.8068 (mmt) REVERT: C 260 TYR cc_start: 0.7311 (t80) cc_final: 0.7010 (t80) REVERT: D 78 VAL cc_start: 0.7576 (t) cc_final: 0.7324 (p) REVERT: D 117 MET cc_start: 0.6813 (ttm) cc_final: 0.6606 (mtp) REVERT: D 272 MET cc_start: 0.8270 (mmm) cc_final: 0.7986 (mmm) REVERT: D 292 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7038 (mp0) REVERT: D 309 MET cc_start: 0.7714 (mtp) cc_final: 0.7510 (mtp) REVERT: D 330 THR cc_start: 0.6072 (m) cc_final: 0.5705 (p) REVERT: E 35 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7810 (mtmt) REVERT: E 84 SER cc_start: 0.8186 (p) cc_final: 0.7848 (t) REVERT: E 89 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6134 (mm-30) REVERT: E 143 ARG cc_start: 0.6296 (mtm180) cc_final: 0.5971 (mtm110) REVERT: E 179 GLU cc_start: 0.7609 (pt0) cc_final: 0.7356 (pt0) REVERT: E 255 HIS cc_start: 0.6778 (p-80) cc_final: 0.6182 (m90) REVERT: E 267 ARG cc_start: 0.7189 (ttm-80) cc_final: 0.6630 (ttp-110) REVERT: E 301 TYR cc_start: 0.7064 (t80) cc_final: 0.6821 (t80) REVERT: F 102 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6765 (mp0) REVERT: F 125 SER cc_start: 0.8235 (m) cc_final: 0.8028 (p) REVERT: F 144 SER cc_start: 0.8689 (p) cc_final: 0.8426 (t) REVERT: F 267 ARG cc_start: 0.6497 (ttm170) cc_final: 0.5865 (ttp80) REVERT: F 286 ASN cc_start: 0.7033 (m-40) cc_final: 0.6809 (m110) outliers start: 15 outliers final: 13 residues processed: 279 average time/residue: 0.6703 time to fit residues: 268.4933 Evaluate side-chains 264 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.027 16228 Z= 0.181 Angle : 0.506 5.778 22105 Z= 0.274 Chirality : 0.039 0.142 2498 Planarity : 0.005 0.054 2739 Dihedral : 15.137 167.493 2563 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.94 % Allowed : 6.24 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.10 (0.19), residues: 1902 helix: 0.86 (0.16), residues: 1050 sheet: 1.27 (0.31), residues: 272 loop : 0.49 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 146 PHE 0.006 0.001 PHE B 58 TYR 0.010 0.001 TYR D 131 ARG 0.005 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 269 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.8763 (p90) cc_final: 0.8218 (p90) REVERT: A 234 MET cc_start: 0.7374 (ptp) cc_final: 0.6852 (ptp) REVERT: A 252 ASP cc_start: 0.7574 (t0) cc_final: 0.7078 (t0) REVERT: A 282 THR cc_start: 0.7914 (m) cc_final: 0.7705 (p) REVERT: A 309 MET cc_start: 0.7268 (ttm) cc_final: 0.7058 (ttt) REVERT: A 325 MET cc_start: 0.7624 (mmm) cc_final: 0.7275 (mmt) REVERT: B 102 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7079 (mt-10) REVERT: B 128 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: B 199 MET cc_start: 0.8013 (mmp) cc_final: 0.7258 (tpt) REVERT: B 234 MET cc_start: 0.8307 (mmp) cc_final: 0.7974 (mmt) REVERT: C 178 MET cc_start: 0.8722 (mmt) cc_final: 0.8165 (mmt) REVERT: D 78 VAL cc_start: 0.7553 (t) cc_final: 0.7317 (p) REVERT: D 130 TYR cc_start: 0.5561 (m-80) cc_final: 0.5298 (m-80) REVERT: D 272 MET cc_start: 0.8293 (mmm) cc_final: 0.8026 (mmm) REVERT: D 292 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7081 (mp0) REVERT: D 330 THR cc_start: 0.6068 (m) cc_final: 0.5718 (p) REVERT: E 84 SER cc_start: 0.8078 (p) cc_final: 0.7756 (t) REVERT: E 89 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5960 (mm-30) REVERT: E 143 ARG cc_start: 0.6337 (mtm180) cc_final: 0.5978 (mtm110) REVERT: E 179 GLU cc_start: 0.7636 (pt0) cc_final: 0.7356 (pt0) REVERT: E 255 HIS cc_start: 0.6775 (p-80) cc_final: 0.6203 (m90) REVERT: E 267 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6568 (ttp-110) REVERT: E 301 TYR cc_start: 0.7205 (t80) cc_final: 0.6885 (t80) REVERT: E 309 MET cc_start: 0.4172 (ptt) cc_final: 0.3915 (ptt) REVERT: F 102 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6779 (mp0) REVERT: F 125 SER cc_start: 0.8261 (m) cc_final: 0.8057 (p) REVERT: F 286 ASN cc_start: 0.7054 (m-40) cc_final: 0.6692 (m110) outliers start: 15 outliers final: 12 residues processed: 276 average time/residue: 0.7357 time to fit residues: 290.0289 Evaluate side-chains 263 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.219 Angle : 0.514 6.265 22105 Z= 0.278 Chirality : 0.040 0.183 2498 Planarity : 0.005 0.047 2739 Dihedral : 15.153 169.669 2563 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.00 % Allowed : 6.92 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.19 (0.19), residues: 1902 helix: 1.05 (0.16), residues: 1049 sheet: 1.12 (0.30), residues: 268 loop : 0.39 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 146 PHE 0.006 0.001 PHE B 152 TYR 0.009 0.001 TYR D 131 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 2.651 Fit side-chains REVERT: A 100 ASP cc_start: 0.7812 (m-30) cc_final: 0.7552 (t70) REVERT: A 131 TYR cc_start: 0.8756 (p90) cc_final: 0.8219 (p90) REVERT: A 144 SER cc_start: 0.8080 (p) cc_final: 0.7847 (t) REVERT: A 199 MET cc_start: 0.8087 (mmt) cc_final: 0.7809 (mmt) REVERT: A 234 MET cc_start: 0.7358 (ptp) cc_final: 0.6783 (ptp) REVERT: A 252 ASP cc_start: 0.7592 (t0) cc_final: 0.7015 (t0) REVERT: A 309 MET cc_start: 0.7204 (ttm) cc_final: 0.6994 (ttt) REVERT: A 325 MET cc_start: 0.7645 (mmm) cc_final: 0.7291 (mmt) REVERT: B 102 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7149 (mt-10) REVERT: B 128 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: B 199 MET cc_start: 0.8121 (mmp) cc_final: 0.7379 (tpt) REVERT: B 234 MET cc_start: 0.8381 (mmp) cc_final: 0.8005 (mmt) REVERT: C 178 MET cc_start: 0.8729 (mmt) cc_final: 0.8272 (mmt) REVERT: D 78 VAL cc_start: 0.7608 (t) cc_final: 0.7326 (p) REVERT: D 272 MET cc_start: 0.8310 (mmm) cc_final: 0.8061 (mmm) REVERT: D 292 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7141 (mp0) REVERT: D 330 THR cc_start: 0.6362 (m) cc_final: 0.6020 (p) REVERT: E 84 SER cc_start: 0.8044 (p) cc_final: 0.7777 (t) REVERT: E 89 GLU cc_start: 0.6705 (mt-10) cc_final: 0.5977 (mm-30) REVERT: E 143 ARG cc_start: 0.6392 (mtm180) cc_final: 0.6028 (mtm110) REVERT: E 179 GLU cc_start: 0.7615 (pt0) cc_final: 0.7298 (pt0) REVERT: E 255 HIS cc_start: 0.6798 (p-80) cc_final: 0.6242 (m90) REVERT: E 260 TYR cc_start: 0.7075 (t80) cc_final: 0.6696 (t80) REVERT: E 267 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6553 (ttp-110) REVERT: E 301 TYR cc_start: 0.7194 (t80) cc_final: 0.6908 (t80) REVERT: E 309 MET cc_start: 0.4205 (ptt) cc_final: 0.3961 (ptt) REVERT: F 102 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6806 (mp0) outliers start: 16 outliers final: 11 residues processed: 260 average time/residue: 0.6993 time to fit residues: 265.0757 Evaluate side-chains 254 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16228 Z= 0.235 Angle : 0.513 5.861 22105 Z= 0.277 Chirality : 0.040 0.141 2498 Planarity : 0.005 0.046 2739 Dihedral : 15.198 171.312 2563 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.00 % Allowed : 8.05 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.21 (0.19), residues: 1902 helix: 1.12 (0.16), residues: 1048 sheet: 1.03 (0.31), residues: 268 loop : 0.33 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 146 PHE 0.007 0.001 PHE A 152 TYR 0.019 0.001 TYR A 329 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 247 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7816 (m-30) cc_final: 0.7567 (t70) REVERT: A 114 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8150 (mmp80) REVERT: A 131 TYR cc_start: 0.8750 (p90) cc_final: 0.8150 (p90) REVERT: A 144 SER cc_start: 0.8021 (p) cc_final: 0.7746 (t) REVERT: A 199 MET cc_start: 0.8196 (mmt) cc_final: 0.7972 (mmt) REVERT: A 234 MET cc_start: 0.7490 (ptp) cc_final: 0.6872 (ptp) REVERT: A 252 ASP cc_start: 0.7595 (t0) cc_final: 0.7009 (t0) REVERT: A 309 MET cc_start: 0.7200 (ttm) cc_final: 0.6989 (ttt) REVERT: A 325 MET cc_start: 0.7677 (mmm) cc_final: 0.7319 (mmt) REVERT: B 102 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7170 (mt-10) REVERT: B 128 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: B 199 MET cc_start: 0.8137 (mmp) cc_final: 0.7352 (tpt) REVERT: B 234 MET cc_start: 0.8419 (mmp) cc_final: 0.8007 (mmt) REVERT: B 242 LYS cc_start: 0.7674 (tppt) cc_final: 0.7132 (tppt) REVERT: C 178 MET cc_start: 0.8732 (mmt) cc_final: 0.8273 (mmt) REVERT: D 78 VAL cc_start: 0.7721 (t) cc_final: 0.7440 (p) REVERT: D 272 MET cc_start: 0.8322 (mmm) cc_final: 0.8007 (mmm) REVERT: D 292 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7202 (mp0) REVERT: D 330 THR cc_start: 0.6491 (m) cc_final: 0.6130 (p) REVERT: E 84 SER cc_start: 0.8061 (p) cc_final: 0.7855 (t) REVERT: E 89 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6141 (mm-30) REVERT: E 143 ARG cc_start: 0.6345 (mtm180) cc_final: 0.6031 (mtm110) REVERT: E 179 GLU cc_start: 0.7598 (pt0) cc_final: 0.7304 (pt0) REVERT: E 255 HIS cc_start: 0.6765 (p-80) cc_final: 0.6291 (m90) REVERT: E 267 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6608 (ttp-110) REVERT: E 301 TYR cc_start: 0.7183 (t80) cc_final: 0.6925 (t80) REVERT: E 309 MET cc_start: 0.4111 (ptt) cc_final: 0.3868 (ptt) REVERT: F 102 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6814 (mp0) outliers start: 16 outliers final: 14 residues processed: 254 average time/residue: 0.7079 time to fit residues: 259.6199 Evaluate side-chains 258 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16228 Z= 0.257 Angle : 0.525 5.928 22105 Z= 0.283 Chirality : 0.041 0.215 2498 Planarity : 0.005 0.047 2739 Dihedral : 15.246 173.500 2563 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.25 % Allowed : 8.42 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.10 (0.19), residues: 1902 helix: 1.10 (0.16), residues: 1049 sheet: 0.90 (0.30), residues: 274 loop : 0.17 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 54 PHE 0.007 0.001 PHE B 58 TYR 0.010 0.001 TYR D 124 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 2.690 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7791 (m-30) cc_final: 0.7565 (t70) REVERT: A 131 TYR cc_start: 0.8733 (p90) cc_final: 0.8150 (p90) REVERT: A 144 SER cc_start: 0.7973 (p) cc_final: 0.7523 (t) REVERT: A 234 MET cc_start: 0.7499 (ptp) cc_final: 0.6973 (ptp) REVERT: A 252 ASP cc_start: 0.7615 (t0) cc_final: 0.7015 (t0) REVERT: A 309 MET cc_start: 0.7220 (ttm) cc_final: 0.6986 (ttt) REVERT: A 325 MET cc_start: 0.7688 (mmm) cc_final: 0.7336 (mmt) REVERT: B 102 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7155 (mt-10) REVERT: B 128 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6659 (tt0) REVERT: B 199 MET cc_start: 0.8233 (mmp) cc_final: 0.7438 (tpt) REVERT: B 234 MET cc_start: 0.8415 (mmp) cc_final: 0.7994 (mmt) REVERT: B 242 LYS cc_start: 0.7659 (tppt) cc_final: 0.7118 (tppt) REVERT: C 78 VAL cc_start: 0.8668 (t) cc_final: 0.8392 (p) REVERT: C 178 MET cc_start: 0.8711 (mmt) cc_final: 0.8149 (mmt) REVERT: D 272 MET cc_start: 0.8308 (mmm) cc_final: 0.7952 (mmm) REVERT: D 292 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7225 (mp0) REVERT: E 89 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6100 (mm-30) REVERT: E 143 ARG cc_start: 0.6390 (mtm180) cc_final: 0.6071 (mtm110) REVERT: E 179 GLU cc_start: 0.7679 (pt0) cc_final: 0.7381 (pt0) REVERT: E 255 HIS cc_start: 0.6968 (p-80) cc_final: 0.6358 (m90) REVERT: E 260 TYR cc_start: 0.7131 (t80) cc_final: 0.6723 (t80) REVERT: E 267 ARG cc_start: 0.6904 (ttm-80) cc_final: 0.6433 (ttp-110) REVERT: E 301 TYR cc_start: 0.7187 (t80) cc_final: 0.6947 (t80) REVERT: E 309 MET cc_start: 0.4115 (ptt) cc_final: 0.3875 (ptt) REVERT: F 102 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6879 (mp0) outliers start: 20 outliers final: 17 residues processed: 256 average time/residue: 0.6945 time to fit residues: 256.1259 Evaluate side-chains 255 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 115 optimal weight: 0.0040 chunk 112 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.167 Angle : 0.485 5.789 22105 Z= 0.260 Chirality : 0.039 0.141 2498 Planarity : 0.005 0.038 2739 Dihedral : 15.183 172.627 2563 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.12 % Allowed : 8.98 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.33 (0.19), residues: 1902 helix: 1.30 (0.17), residues: 1049 sheet: 0.89 (0.30), residues: 274 loop : 0.29 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 146 PHE 0.006 0.001 PHE B 58 TYR 0.012 0.001 TYR D 131 ARG 0.006 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6953 (mp0) REVERT: A 131 TYR cc_start: 0.8725 (p90) cc_final: 0.8161 (p90) REVERT: A 144 SER cc_start: 0.7939 (p) cc_final: 0.7483 (t) REVERT: A 234 MET cc_start: 0.7331 (ptp) cc_final: 0.6790 (ptp) REVERT: A 252 ASP cc_start: 0.7604 (t0) cc_final: 0.6998 (t0) REVERT: A 309 MET cc_start: 0.7199 (ttm) cc_final: 0.6970 (ttt) REVERT: A 325 MET cc_start: 0.7545 (mmm) cc_final: 0.7300 (mmt) REVERT: B 102 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7167 (mt-10) REVERT: B 128 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: B 133 ASP cc_start: 0.7572 (m-30) cc_final: 0.7317 (m-30) REVERT: B 199 MET cc_start: 0.8251 (mmp) cc_final: 0.7447 (tpt) REVERT: B 234 MET cc_start: 0.8387 (mmp) cc_final: 0.7945 (mmt) REVERT: B 242 LYS cc_start: 0.7707 (tppt) cc_final: 0.7141 (tppt) REVERT: C 78 VAL cc_start: 0.8638 (t) cc_final: 0.8376 (p) REVERT: C 178 MET cc_start: 0.8719 (mmt) cc_final: 0.8261 (mmt) REVERT: D 272 MET cc_start: 0.8285 (mmm) cc_final: 0.7925 (mmm) REVERT: D 292 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7222 (mp0) REVERT: E 89 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6121 (mm-30) REVERT: E 143 ARG cc_start: 0.6388 (mtm180) cc_final: 0.6070 (mtm110) REVERT: E 179 GLU cc_start: 0.7676 (pt0) cc_final: 0.7381 (pt0) REVERT: E 240 ASP cc_start: 0.6880 (m-30) cc_final: 0.5987 (t70) REVERT: E 255 HIS cc_start: 0.6930 (p-80) cc_final: 0.6338 (m90) REVERT: E 260 TYR cc_start: 0.7078 (t80) cc_final: 0.6716 (t80) REVERT: E 267 ARG cc_start: 0.6952 (ttm-80) cc_final: 0.6505 (ttp-110) REVERT: E 301 TYR cc_start: 0.7207 (t80) cc_final: 0.6975 (t80) REVERT: E 309 MET cc_start: 0.4124 (ptt) cc_final: 0.3872 (ptt) REVERT: F 102 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6873 (mp0) outliers start: 18 outliers final: 14 residues processed: 252 average time/residue: 0.6741 time to fit residues: 244.5267 Evaluate side-chains 252 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.0000 chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16228 Z= 0.278 Angle : 0.534 5.961 22105 Z= 0.287 Chirality : 0.041 0.143 2498 Planarity : 0.005 0.048 2739 Dihedral : 15.270 176.103 2563 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.12 % Allowed : 9.05 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.11 (0.19), residues: 1902 helix: 1.14 (0.16), residues: 1052 sheet: 0.80 (0.30), residues: 272 loop : 0.17 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.008 0.001 PHE A 152 TYR 0.010 0.001 TYR E 131 ARG 0.005 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6978 (mp0) REVERT: A 131 TYR cc_start: 0.8728 (p90) cc_final: 0.8073 (p90) REVERT: A 144 SER cc_start: 0.7937 (p) cc_final: 0.7490 (t) REVERT: A 234 MET cc_start: 0.7451 (ptp) cc_final: 0.6937 (ptp) REVERT: A 252 ASP cc_start: 0.7654 (t0) cc_final: 0.7048 (t0) REVERT: A 309 MET cc_start: 0.7256 (ttm) cc_final: 0.7024 (ttt) REVERT: A 325 MET cc_start: 0.7589 (mmm) cc_final: 0.7321 (mmt) REVERT: B 102 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7218 (mt-10) REVERT: B 128 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: B 199 MET cc_start: 0.8211 (mmp) cc_final: 0.7399 (tpt) REVERT: B 242 LYS cc_start: 0.7727 (tppt) cc_final: 0.7151 (tppt) REVERT: D 272 MET cc_start: 0.8343 (mmm) cc_final: 0.7992 (mmm) REVERT: D 292 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7289 (mp0) REVERT: E 89 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6045 (mm-30) REVERT: E 143 ARG cc_start: 0.6466 (mtm180) cc_final: 0.6148 (mtm110) REVERT: E 179 GLU cc_start: 0.7635 (pt0) cc_final: 0.7292 (pt0) REVERT: E 240 ASP cc_start: 0.6937 (m-30) cc_final: 0.6026 (t70) REVERT: E 255 HIS cc_start: 0.6998 (p-80) cc_final: 0.6307 (m90) REVERT: E 260 TYR cc_start: 0.7136 (t80) cc_final: 0.6731 (t80) REVERT: E 267 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6465 (ttp-110) REVERT: E 301 TYR cc_start: 0.7190 (t80) cc_final: 0.6959 (t80) REVERT: E 309 MET cc_start: 0.4149 (ptt) cc_final: 0.3881 (ptt) REVERT: F 102 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6942 (mp0) outliers start: 18 outliers final: 17 residues processed: 250 average time/residue: 0.7212 time to fit residues: 257.3959 Evaluate side-chains 256 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 170 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16228 Z= 0.161 Angle : 0.482 7.193 22105 Z= 0.258 Chirality : 0.039 0.137 2498 Planarity : 0.005 0.038 2739 Dihedral : 15.199 174.163 2563 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.00 % Allowed : 9.23 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.41 (0.19), residues: 1902 helix: 1.38 (0.17), residues: 1050 sheet: 0.91 (0.30), residues: 272 loop : 0.31 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.006 0.001 PHE E 58 TYR 0.010 0.001 TYR D 131 ARG 0.004 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 240 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 131 TYR cc_start: 0.8742 (p90) cc_final: 0.8183 (p90) REVERT: A 144 SER cc_start: 0.7885 (p) cc_final: 0.7432 (t) REVERT: A 234 MET cc_start: 0.7330 (ptp) cc_final: 0.6813 (ptp) REVERT: A 252 ASP cc_start: 0.7613 (t0) cc_final: 0.6999 (t0) REVERT: A 309 MET cc_start: 0.7192 (ttm) cc_final: 0.6970 (ttt) REVERT: A 325 MET cc_start: 0.7553 (mmm) cc_final: 0.7311 (mmt) REVERT: B 102 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7215 (mt-10) REVERT: B 199 MET cc_start: 0.8133 (mmp) cc_final: 0.7324 (tpt) REVERT: B 242 LYS cc_start: 0.7685 (tppt) cc_final: 0.7115 (tppt) REVERT: C 178 MET cc_start: 0.8688 (mmt) cc_final: 0.8183 (mmt) REVERT: D 79 ASN cc_start: 0.7637 (m-40) cc_final: 0.7401 (m110) REVERT: D 272 MET cc_start: 0.8306 (mmm) cc_final: 0.7945 (mmm) REVERT: D 292 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7281 (mp0) REVERT: E 89 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6245 (mm-30) REVERT: E 143 ARG cc_start: 0.6394 (mtm180) cc_final: 0.6076 (mtm110) REVERT: E 179 GLU cc_start: 0.7629 (pt0) cc_final: 0.7292 (pt0) REVERT: E 240 ASP cc_start: 0.6879 (m-30) cc_final: 0.6022 (t70) REVERT: E 255 HIS cc_start: 0.6936 (p-80) cc_final: 0.6288 (m90) REVERT: E 260 TYR cc_start: 0.7088 (t80) cc_final: 0.6717 (t80) REVERT: E 267 ARG cc_start: 0.6960 (ttm-80) cc_final: 0.6528 (ttp-110) REVERT: E 309 MET cc_start: 0.4132 (ptt) cc_final: 0.3871 (ptt) REVERT: F 102 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6905 (mp0) REVERT: F 195 GLU cc_start: 0.6998 (tp30) cc_final: 0.6679 (tp30) outliers start: 16 outliers final: 14 residues processed: 248 average time/residue: 0.6996 time to fit residues: 250.7399 Evaluate side-chains 248 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16228 Z= 0.240 Angle : 0.510 6.625 22105 Z= 0.274 Chirality : 0.040 0.140 2498 Planarity : 0.005 0.041 2739 Dihedral : 15.238 175.460 2563 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.81 % Allowed : 9.48 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.33 (0.19), residues: 1902 helix: 1.33 (0.16), residues: 1048 sheet: 0.85 (0.30), residues: 272 loop : 0.26 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 54 PHE 0.007 0.001 PHE A 152 TYR 0.010 0.001 TYR D 131 ARG 0.004 0.000 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6979 (mp0) REVERT: A 131 TYR cc_start: 0.8745 (p90) cc_final: 0.8179 (p90) REVERT: A 144 SER cc_start: 0.7896 (p) cc_final: 0.7439 (t) REVERT: A 234 MET cc_start: 0.7449 (ptp) cc_final: 0.6921 (ptp) REVERT: A 252 ASP cc_start: 0.7624 (t0) cc_final: 0.6997 (t0) REVERT: A 309 MET cc_start: 0.7221 (ttm) cc_final: 0.6998 (ttt) REVERT: A 312 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6751 (tpt170) REVERT: A 325 MET cc_start: 0.7578 (mmm) cc_final: 0.7327 (mmt) REVERT: B 102 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7167 (mt-10) REVERT: B 199 MET cc_start: 0.8177 (mmp) cc_final: 0.7413 (tpt) REVERT: B 242 LYS cc_start: 0.7692 (tppt) cc_final: 0.7113 (tppt) REVERT: C 178 MET cc_start: 0.8681 (mmt) cc_final: 0.8196 (mmt) REVERT: D 272 MET cc_start: 0.8328 (mmm) cc_final: 0.7970 (mmm) REVERT: D 292 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7266 (mp0) REVERT: E 89 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6242 (mm-30) REVERT: E 143 ARG cc_start: 0.6467 (mtm180) cc_final: 0.6151 (mtm110) REVERT: E 179 GLU cc_start: 0.7649 (pt0) cc_final: 0.7310 (pt0) REVERT: E 240 ASP cc_start: 0.6901 (m-30) cc_final: 0.6034 (t70) REVERT: E 255 HIS cc_start: 0.7000 (p-80) cc_final: 0.6329 (m90) REVERT: E 260 TYR cc_start: 0.7127 (t80) cc_final: 0.6742 (t80) REVERT: E 267 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6460 (ttp-110) REVERT: E 309 MET cc_start: 0.4149 (ptt) cc_final: 0.3907 (ptt) REVERT: F 102 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6862 (mp0) outliers start: 13 outliers final: 13 residues processed: 242 average time/residue: 0.6781 time to fit residues: 235.5152 Evaluate side-chains 247 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092926 restraints weight = 65789.720| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.99 r_work: 0.2811 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.219 Angle : 0.505 7.047 22105 Z= 0.270 Chirality : 0.040 0.139 2498 Planarity : 0.005 0.043 2739 Dihedral : 15.265 176.151 2563 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.87 % Allowed : 9.48 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.33 (0.19), residues: 1902 helix: 1.33 (0.16), residues: 1048 sheet: 0.85 (0.30), residues: 271 loop : 0.26 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.007 0.001 PHE B 58 TYR 0.011 0.001 TYR D 131 ARG 0.004 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7420.17 seconds wall clock time: 129 minutes 17.59 seconds (7757.59 seconds total)