Starting phenix.real_space_refine on Wed Aug 7 20:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh9_39285/08_2024/8yh9_39285.cif" } resolution = 3.35 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= -0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 103 5.16 5 C 13307 2.51 5 N 3539 2.21 5 O 4145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 184": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "I GLU 309": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "F TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "J PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21153 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 8, 'rna3p_pur': 21, 'rna3p_pyr': 14} Link IDs: {'rna2p': 23, 'rna3p': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2467 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2423 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "G" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2461 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2447 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "E" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2397 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2393 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Chain: "J" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 12.46, per 1000 atoms: 0.59 Number of scatterers: 21153 At special positions: 0 Unit cell: (119, 153, 153.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 59 15.00 O 4145 8.00 N 3539 7.00 C 13307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 3.5 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4666 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 32 sheets defined 28.4% alpha, 16.3% beta 5 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 removed outlier: 4.166A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.116A pdb=" N GLU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.134A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HIS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 24 through 35 removed outlier: 4.743A pdb=" N SER B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.732A pdb=" N LEU B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.693A pdb=" N HIS B 76 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.796A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.736A pdb=" N ALA I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG I 137 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 177 removed outlier: 3.668A pdb=" N PHE I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 202 removed outlier: 3.994A pdb=" N THR I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.847A pdb=" N ALA I 257 " --> pdb=" O LYS I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 271 Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'H' and resid 111 through 127 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.677A pdb=" N LYS H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 177 removed outlier: 3.661A pdb=" N PHE H 177 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 200 Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.617A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.895A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 303 removed outlier: 3.601A pdb=" N ASP H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.689A pdb=" N GLN G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.536A pdb=" N ALA G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.739A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.866A pdb=" N LEU G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 removed outlier: 3.720A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 200 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.558A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 4.018A pdb=" N VAL G 319 " --> pdb=" O ASP G 315 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET G 320 " --> pdb=" O LYS G 316 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG G 325 " --> pdb=" O ALA G 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.370A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 116 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.526A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.536A pdb=" N GLY F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 4.038A pdb=" N ILE F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 256 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.813A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 305 removed outlier: 3.757A pdb=" N ARG F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 303 Processing helix chain 'E' and resid 313 through 326 removed outlier: 4.050A pdb=" N TYR E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.638A pdb=" N MET D 106 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.614A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 188 through 202 removed outlier: 4.341A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.680A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.915A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'J' and resid 166 through 179 removed outlier: 3.837A pdb=" N SER J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP J 175 " --> pdb=" O TYR J 171 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG J 179 " --> pdb=" O ASP J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 199 removed outlier: 3.662A pdb=" N ALA J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 206 removed outlier: 3.580A pdb=" N ASN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 229 Processing helix chain 'J' and resid 255 through 264 Processing helix chain 'J' and resid 283 through 291 Processing helix chain 'J' and resid 324 through 339 removed outlier: 3.895A pdb=" N GLU J 333 " --> pdb=" O GLU J 329 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA J 336 " --> pdb=" O THR J 332 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 4.106A pdb=" N GLY A 54 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 113 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 52 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLU A 219 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE A 196 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 221 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 removed outlier: 4.123A pdb=" N LYS A 10 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET A 106 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 104 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A 14 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 102 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 54 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 113 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 52 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 220 " --> pdb=" O LEU J 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.357A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.864A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 102 removed outlier: 4.010A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 158 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 106 through 109 removed outlier: 3.678A pdb=" N SER I 108 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.507A pdb=" N THR I 35 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 94 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS I 31 " --> pdb=" O ASP I 94 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 30 through 35 current: chain 'I' and resid 161 through 164 Processing sheet with id=AB2, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.669A pdb=" N LYS I 31 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 94 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR I 35 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 50 through 53 removed outlier: 3.975A pdb=" N SER I 79 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.713A pdb=" N ARG H 92 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP H 94 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 31 " --> pdb=" O ASP H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AB6, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AB7, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.590A pdb=" N LYS G 31 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP G 94 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE G 95 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL G 211 " --> pdb=" O PHE G 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 50 through 55 Processing sheet with id=AC1, first strand: chain 'G' and resid 163 through 164 removed outlier: 3.642A pdb=" N ILE G 164 " --> pdb=" O LYS G 167 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 21 removed outlier: 4.082A pdb=" N GLY F 327 " --> pdb=" O PHE F 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.549A pdb=" N LYS F 31 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 164 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 45 through 46 removed outlier: 5.527A pdb=" N ALA F 247 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.518A pdb=" N LYS F 52 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER F 79 " --> pdb=" O LYS F 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.568A pdb=" N MET E 249 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA E 247 " --> pdb=" O PHE E 32 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AD1, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.699A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 30 through 35 current: chain 'D' and resid 158 through 163 Processing sheet with id=AD2, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.699A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AD4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'J' and resid 185 through 186 599 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5369 1.33 - 1.45: 4403 1.45 - 1.57: 11687 1.57 - 1.69: 118 1.69 - 1.81: 159 Bond restraints: 21736 Sorted by residual: bond pdb=" CB TYR F 125 " pdb=" CG TYR F 125 " ideal model delta sigma weight residual 1.512 1.560 -0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" N ASP I 310 " pdb=" CA ASP I 310 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.60e+00 bond pdb=" CG1 ILE E 93 " pdb=" CD1 ILE E 93 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.90e+00 bond pdb=" C ARG B 125 " pdb=" N PRO B 126 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.80e+00 bond pdb=" CA ASN F 18 " pdb=" CB ASN F 18 " ideal model delta sigma weight residual 1.527 1.568 -0.041 2.48e-02 1.63e+03 2.72e+00 ... (remaining 21731 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.57: 623 105.57 - 112.68: 11142 112.68 - 119.80: 7528 119.80 - 126.91: 9993 126.91 - 134.03: 353 Bond angle restraints: 29639 Sorted by residual: angle pdb=" C SER G 174 " pdb=" N LYS G 175 " pdb=" CA LYS G 175 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA TYR F 125 " pdb=" CB TYR F 125 " pdb=" CG TYR F 125 " ideal model delta sigma weight residual 113.90 120.75 -6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C SER A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CA GLU I 278 " pdb=" CB GLU I 278 " pdb=" CG GLU I 278 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CA TYR E 112 " pdb=" CB TYR E 112 " pdb=" CG TYR E 112 " ideal model delta sigma weight residual 113.90 120.43 -6.53 1.80e+00 3.09e-01 1.32e+01 ... (remaining 29634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12342 35.97 - 71.94: 781 71.94 - 107.92: 50 107.92 - 143.89: 0 143.89 - 179.86: 2 Dihedral angle restraints: 13175 sinusoidal: 5951 harmonic: 7224 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual -128.00 51.86 -179.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 44 " pdb=" C1' U C 44 " pdb=" N1 U C 44 " pdb=" C2 U C 44 " ideal model delta sinusoidal sigma weight residual 232.00 54.13 177.87 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -160.00 -84.86 -75.14 1 1.50e+01 4.44e-03 3.17e+01 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2564 0.056 - 0.112: 609 0.112 - 0.167: 120 0.167 - 0.223: 7 0.223 - 0.279: 3 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CB ILE E 93 " pdb=" CA ILE E 93 " pdb=" CG1 ILE E 93 " pdb=" CG2 ILE E 93 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE I 93 " pdb=" CA ILE I 93 " pdb=" CG1 ILE I 93 " pdb=" CG2 ILE I 93 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE E 97 " pdb=" CA ILE E 97 " pdb=" CG1 ILE E 97 " pdb=" CG2 ILE E 97 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3300 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 9 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO B 10 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 174 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER G 174 " 0.053 2.00e-02 2.50e+03 pdb=" O SER G 174 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 175 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 256 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO J 257 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " 0.043 5.00e-02 4.00e+02 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5084 2.79 - 3.32: 18147 3.32 - 3.84: 35903 3.84 - 4.37: 39871 4.37 - 4.90: 68785 Nonbonded interactions: 167790 Sorted by model distance: nonbonded pdb=" O LEU A 80 " pdb=" O2' A C 7 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR F 265 " pdb=" O PHE F 273 " model vdw 2.268 3.040 nonbonded pdb=" O ALA F 143 " pdb=" OG SER F 174 " model vdw 2.269 3.040 nonbonded pdb=" OG SER B 148 " pdb=" O THR B 151 " model vdw 2.275 3.040 nonbonded pdb=" O THR D 28 " pdb=" OG SER D 251 " model vdw 2.277 3.040 ... (remaining 167785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 18 through 330) selection = (chain 'E' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'F' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'G' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'H' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'I' and (resid 18 through 53 or resid 79 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: 5.980 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: 0.000 Extract box with map and model: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 60.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.004 0.066 21736 Z= 0.254 Angle : 0.761 9.959 29639 Z= 0.413 Chirality : 0.049 0.279 3303 Planarity : 0.006 0.107 3558 Dihedral : 20.726 179.860 8509 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.65 % Allowed : 39.19 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.15), residues: 2416 helix: -1.97 (0.17), residues: 616 sheet: -0.29 (0.29), residues: 357 loop : -2.52 (0.14), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 33 HIS 0.007 0.001 HIS A 204 PHE 0.035 0.002 PHE G 200 TYR 0.031 0.002 TYR I 206 ARG 0.011 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 291 average time/residue: 0.2940 time to fit residues: 136.6204 Evaluate side-chains 268 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain D residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 0.0010 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 194 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 250 HIS J 145 GLN J 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21736 Z= 0.169 Angle : 0.533 9.353 29639 Z= 0.283 Chirality : 0.040 0.201 3303 Planarity : 0.004 0.072 3558 Dihedral : 14.929 179.599 3596 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.36 % Allowed : 37.13 % Favored : 58.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2416 helix: -1.08 (0.19), residues: 642 sheet: 0.00 (0.32), residues: 313 loop : -2.45 (0.14), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.004 0.001 HIS D 317 PHE 0.021 0.001 PHE G 200 TYR 0.016 0.001 TYR D 125 ARG 0.004 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 279 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6560 (mp10) REVERT: I 91 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7352 (pt) REVERT: I 158 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6485 (mt) REVERT: H 47 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8149 (mp) outliers start: 95 outliers final: 45 residues processed: 345 average time/residue: 0.2940 time to fit residues: 164.0624 Evaluate side-chains 306 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 225 optimal weight: 0.1980 chunk 243 optimal weight: 0.0470 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 overall best weight: 2.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 215 HIS I 140 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 34 GLN G 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN D 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21736 Z= 0.234 Angle : 0.565 12.223 29639 Z= 0.297 Chirality : 0.042 0.192 3303 Planarity : 0.004 0.060 3558 Dihedral : 14.856 177.708 3583 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.83 % Allowed : 35.89 % Favored : 58.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2416 helix: -0.76 (0.20), residues: 635 sheet: -0.10 (0.32), residues: 314 loop : -2.42 (0.14), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.007 0.001 HIS E 250 PHE 0.022 0.002 PHE G 200 TYR 0.019 0.001 TYR E 112 ARG 0.004 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 266 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: I 158 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6625 (mt) REVERT: H 112 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.3829 (m-10) REVERT: G 328 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.2248 (tpp) REVERT: F 159 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: F 329 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: E 151 ASN cc_start: 0.7605 (m-40) cc_final: 0.7364 (m110) outliers start: 127 outliers final: 72 residues processed: 358 average time/residue: 0.2903 time to fit residues: 168.3681 Evaluate side-chains 330 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 252 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 107 optimal weight: 0.4980 chunk 151 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 239 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 56 ASN I 140 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN F 256 ASN E 41 HIS ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21736 Z= 0.182 Angle : 0.530 11.893 29639 Z= 0.279 Chirality : 0.041 0.197 3303 Planarity : 0.004 0.053 3558 Dihedral : 14.788 176.923 3583 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.97 % Allowed : 36.30 % Favored : 57.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.16), residues: 2416 helix: -0.55 (0.20), residues: 646 sheet: -0.12 (0.32), residues: 312 loop : -2.36 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 250 PHE 0.024 0.001 PHE G 200 TYR 0.012 0.001 TYR D 125 ARG 0.005 0.000 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 268 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6375 (mp10) REVERT: B 56 ASN cc_start: 0.5334 (OUTLIER) cc_final: 0.4947 (p0) REVERT: B 129 MET cc_start: 0.3172 (tpp) cc_final: 0.2555 (tpp) REVERT: I 244 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: H 100 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6840 (mt) REVERT: H 112 TYR cc_start: 0.4124 (OUTLIER) cc_final: 0.3553 (m-10) REVERT: H 300 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5310 (pt) REVERT: F 329 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: E 95 PHE cc_start: 0.5235 (p90) cc_final: 0.4938 (p90) outliers start: 130 outliers final: 76 residues processed: 363 average time/residue: 0.3202 time to fit residues: 188.1353 Evaluate side-chains 332 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 249 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 204 HIS B 56 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 HIS F 34 GLN E 41 HIS E 151 ASN D 18 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21736 Z= 0.415 Angle : 0.727 15.650 29639 Z= 0.380 Chirality : 0.047 0.237 3303 Planarity : 0.005 0.051 3558 Dihedral : 15.103 177.257 3583 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 7.66 % Allowed : 34.83 % Favored : 57.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.16), residues: 2416 helix: -1.02 (0.19), residues: 639 sheet: -0.52 (0.31), residues: 328 loop : -2.52 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 149 HIS 0.008 0.001 HIS H 250 PHE 0.063 0.002 PHE G 131 TYR 0.021 0.002 TYR F 107 ARG 0.006 0.001 ARG H 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 256 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6740 (tp) REVERT: A 22 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7085 (tp) REVERT: A 184 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: B 56 ASN cc_start: 0.5488 (p0) cc_final: 0.5152 (p0) REVERT: B 129 MET cc_start: 0.3431 (tpp) cc_final: 0.2744 (tpp) REVERT: I 244 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: H 100 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7062 (mt) REVERT: H 112 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.3828 (m-10) REVERT: H 200 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.5093 (t80) REVERT: H 244 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: G 328 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.3037 (tpp) REVERT: F 21 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: F 329 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: J 74 TRP cc_start: 0.5391 (t60) cc_final: 0.5150 (t60) REVERT: J 146 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5896 (t80) outliers start: 167 outliers final: 111 residues processed: 390 average time/residue: 0.2556 time to fit residues: 160.1584 Evaluate side-chains 367 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 244 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 30.0000 chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN F 256 ASN E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21736 Z= 0.214 Angle : 0.580 13.898 29639 Z= 0.304 Chirality : 0.042 0.193 3303 Planarity : 0.004 0.047 3558 Dihedral : 14.915 175.198 3583 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 7.07 % Allowed : 36.03 % Favored : 56.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2416 helix: -0.71 (0.20), residues: 651 sheet: -0.48 (0.31), residues: 324 loop : -2.42 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 149 HIS 0.004 0.001 HIS E 250 PHE 0.035 0.002 PHE G 131 TYR 0.018 0.001 TYR E 169 ARG 0.004 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 260 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7133 (tp) REVERT: A 99 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: A 184 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: B 129 MET cc_start: 0.3196 (tpp) cc_final: 0.2571 (tpp) REVERT: H 100 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6857 (mt) REVERT: H 112 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3500 (m-10) REVERT: H 200 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.4945 (t80) REVERT: H 207 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5107 (tt) REVERT: H 244 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: G 328 MET cc_start: 0.4278 (OUTLIER) cc_final: 0.2669 (tpp) REVERT: F 21 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: F 329 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: J 74 TRP cc_start: 0.5399 (t60) cc_final: 0.5140 (t60) REVERT: J 146 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5754 (t80) outliers start: 154 outliers final: 99 residues processed: 380 average time/residue: 0.2893 time to fit residues: 175.3321 Evaluate side-chains 360 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 249 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 190 ASN Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.0010 chunk 133 optimal weight: 0.0010 chunk 239 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21736 Z= 0.183 Angle : 0.559 12.679 29639 Z= 0.290 Chirality : 0.041 0.187 3303 Planarity : 0.004 0.047 3558 Dihedral : 14.805 175.543 3583 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.61 % Allowed : 36.67 % Favored : 56.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2416 helix: -0.48 (0.20), residues: 648 sheet: -0.36 (0.31), residues: 317 loop : -2.37 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 149 HIS 0.003 0.001 HIS E 250 PHE 0.022 0.001 PHE G 131 TYR 0.016 0.001 TYR E 169 ARG 0.004 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 260 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 22 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 99 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: A 184 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6143 (mp10) REVERT: B 129 MET cc_start: 0.3103 (tpp) cc_final: 0.2506 (tpp) REVERT: I 244 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6345 (mt-10) REVERT: H 100 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6821 (mt) REVERT: H 112 TYR cc_start: 0.4298 (OUTLIER) cc_final: 0.3467 (m-10) REVERT: H 200 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.4842 (t80) REVERT: H 207 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5042 (tt) REVERT: H 244 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: H 300 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.5086 (pt) REVERT: G 328 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.2610 (tpp) REVERT: F 21 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: F 329 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: J 74 TRP cc_start: 0.5274 (t60) cc_final: 0.5008 (t60) REVERT: J 146 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5681 (t80) outliers start: 144 outliers final: 101 residues processed: 370 average time/residue: 0.2798 time to fit residues: 168.6034 Evaluate side-chains 366 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 250 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 190 ASN Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 40.0000 chunk 151 optimal weight: 0.0870 chunk 162 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21736 Z= 0.251 Angle : 0.603 13.297 29639 Z= 0.312 Chirality : 0.043 0.188 3303 Planarity : 0.004 0.046 3558 Dihedral : 14.819 176.033 3583 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.21 % Allowed : 36.07 % Favored : 56.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.16), residues: 2416 helix: -0.52 (0.20), residues: 644 sheet: -0.51 (0.30), residues: 333 loop : -2.41 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 149 HIS 0.004 0.001 HIS E 250 PHE 0.022 0.002 PHE G 131 TYR 0.031 0.001 TYR E 169 ARG 0.005 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 254 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 22 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7242 (tp) REVERT: A 156 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: A 184 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6104 (mp10) REVERT: B 129 MET cc_start: 0.3159 (tpp) cc_final: 0.2566 (tpp) REVERT: I 244 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: H 100 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6793 (mt) REVERT: H 112 TYR cc_start: 0.4466 (OUTLIER) cc_final: 0.3500 (m-10) REVERT: H 200 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.4887 (t80) REVERT: H 207 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.5150 (tt) REVERT: H 213 CYS cc_start: 0.5671 (t) cc_final: 0.5326 (t) REVERT: H 244 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: H 300 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5284 (pt) REVERT: G 328 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.2685 (tpp) REVERT: F 21 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: J 146 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5675 (t80) outliers start: 157 outliers final: 111 residues processed: 372 average time/residue: 0.2788 time to fit residues: 168.1979 Evaluate side-chains 372 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 247 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 201 optimal weight: 0.0970 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21736 Z= 0.203 Angle : 0.579 12.636 29639 Z= 0.300 Chirality : 0.042 0.188 3303 Planarity : 0.004 0.049 3558 Dihedral : 14.779 175.566 3583 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.42 % Allowed : 36.67 % Favored : 56.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2416 helix: -0.44 (0.20), residues: 641 sheet: -0.51 (0.30), residues: 334 loop : -2.36 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 149 HIS 0.003 0.001 HIS E 250 PHE 0.016 0.001 PHE A 19 TYR 0.043 0.001 TYR E 169 ARG 0.005 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 256 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6744 (tp) REVERT: A 22 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7256 (tp) REVERT: A 99 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: A 184 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6071 (mp10) REVERT: B 129 MET cc_start: 0.3234 (tpp) cc_final: 0.2614 (tpp) REVERT: I 244 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: H 100 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6745 (mt) REVERT: H 112 TYR cc_start: 0.4426 (OUTLIER) cc_final: 0.3465 (m-10) REVERT: H 200 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.4855 (t80) REVERT: H 207 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5158 (tt) REVERT: H 229 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4512 (mtt) REVERT: H 244 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: H 300 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.5231 (pt) REVERT: G 328 MET cc_start: 0.4196 (OUTLIER) cc_final: 0.2631 (tpp) REVERT: F 21 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: J 74 TRP cc_start: 0.5404 (t60) cc_final: 0.5118 (t60) REVERT: J 146 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5655 (t80) outliers start: 140 outliers final: 110 residues processed: 362 average time/residue: 0.2799 time to fit residues: 164.0478 Evaluate side-chains 375 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 250 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21736 Z= 0.251 Angle : 0.621 13.907 29639 Z= 0.318 Chirality : 0.043 0.186 3303 Planarity : 0.004 0.061 3558 Dihedral : 14.802 175.852 3583 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 6.42 % Allowed : 36.35 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2416 helix: -0.49 (0.20), residues: 641 sheet: -0.53 (0.30), residues: 348 loop : -2.39 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 33 HIS 0.004 0.001 HIS H 250 PHE 0.019 0.002 PHE G 131 TYR 0.042 0.001 TYR E 169 ARG 0.008 0.000 ARG E 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 254 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6812 (tp) REVERT: A 22 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7323 (tp) REVERT: A 99 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: A 184 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6111 (mp10) REVERT: A 252 CYS cc_start: 0.6386 (p) cc_final: 0.6008 (p) REVERT: B 129 MET cc_start: 0.3269 (tpp) cc_final: 0.2650 (tpp) REVERT: I 244 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6482 (mt-10) REVERT: H 100 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6830 (mt) REVERT: H 112 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.3549 (m-10) REVERT: H 200 PHE cc_start: 0.5474 (OUTLIER) cc_final: 0.4842 (t80) REVERT: H 207 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5170 (tt) REVERT: H 213 CYS cc_start: 0.5667 (t) cc_final: 0.5326 (t) REVERT: H 244 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: G 328 MET cc_start: 0.4299 (OUTLIER) cc_final: 0.2736 (tpp) REVERT: F 21 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: J 74 TRP cc_start: 0.5437 (t60) cc_final: 0.5159 (t60) REVERT: J 146 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5684 (t80) outliers start: 140 outliers final: 114 residues processed: 360 average time/residue: 0.2760 time to fit residues: 161.7193 Evaluate side-chains 376 residues out of total 2179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 249 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 202 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.195485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.161252 restraints weight = 36287.112| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.82 r_work: 0.3862 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21736 Z= 0.211 Angle : 0.592 12.748 29639 Z= 0.304 Chirality : 0.042 0.186 3303 Planarity : 0.004 0.063 3558 Dihedral : 14.769 175.395 3583 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 6.61 % Allowed : 36.16 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.16), residues: 2416 helix: -0.42 (0.20), residues: 641 sheet: -0.53 (0.30), residues: 349 loop : -2.37 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 33 HIS 0.003 0.001 HIS H 250 PHE 0.019 0.001 PHE A 196 TYR 0.039 0.001 TYR E 169 ARG 0.008 0.000 ARG E 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.55 seconds wall clock time: 88 minutes 32.95 seconds (5312.95 seconds total)