Starting phenix.real_space_refine on Thu Aug 8 16:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ydb_39167/08_2024/8ydb_39167.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 102 5.49 5 S 119 5.16 5 C 14874 2.51 5 N 4010 2.21 5 O 4775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 278": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 185": "OD1" <-> "OD2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E ASP 235": "OD1" <-> "OD2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ASP 261": "OD1" <-> "OD2" Residue "J GLU 282": "OE1" <-> "OE2" Residue "J GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2002 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} 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': 11, 'rna3p_pur': 21, 'rna3p_pyr': 11} Link IDs: {'rna2p': 26, 'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2639 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "H" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "G" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2646 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 15, 'TRANS': 309} Chain: "F" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2628 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "E" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2635 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "D" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2409 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "N" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 12.84, per 1000 atoms: 0.54 Number of scatterers: 23880 At special positions: 0 Unit cell: (138.55, 142.8, 161.5, 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 119 16.00 P 102 15.00 O 4775 8.00 N 4010 7.00 C 14874 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: 8.98 Conformation dependent library (CDL) restraints added in 3.6 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 43 sheets defined 35.1% alpha, 20.1% beta 32 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 7.80 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.844A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.700A pdb=" N LEU A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.702A pdb=" N LEU A 240 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.664A pdb=" N ILE B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.735A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.703A pdb=" N HIS B 76 " --> pdb=" O CYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 123 through 139 removed outlier: 4.505A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 102 through 106 removed outlier: 3.990A pdb=" N MET I 106 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.614A pdb=" N ALA I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 177 removed outlier: 3.580A pdb=" N PHE I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 Processing helix chain 'I' and resid 250 through 259 Processing helix chain 'I' and resid 267 through 271 Processing helix chain 'I' and resid 296 through 305 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.240A pdb=" N GLU H 68 " --> pdb=" O PRO H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 112 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.675A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.555A pdb=" N TRP H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.674A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.682A pdb=" N ASN H 256 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.937A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.650A pdb=" N ASP H 302 " --> pdb=" O TYR H 298 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.756A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.559A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.530A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 153 " --> pdb=" O ARG G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.533A pdb=" N ASN G 256 " --> pdb=" O GLN G 252 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.866A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 307 removed outlier: 3.585A pdb=" N LYS G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.888A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.695A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.503A pdb=" N TRP F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 260 removed outlier: 3.648A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 260 " --> pdb=" O ASN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.962A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.623A pdb=" N ARG E 40 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 removed outlier: 4.496A pdb=" N GLU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.688A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.677A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.733A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.167A pdb=" N TYR E 271 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.648A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.542A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.670A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.529A 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 2 through 10 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.098A pdb=" N GLY J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU J 27 " --> pdb=" O TYR J 23 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE J 28 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN J 29 " --> pdb=" O GLU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 94 removed outlier: 3.835A pdb=" N GLY J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 111 through 122 Processing helix chain 'J' and resid 124 through 134 removed outlier: 4.224A pdb=" N ASN J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 179 Processing helix chain 'J' and resid 191 through 199 removed outlier: 4.038A pdb=" N GLY J 199 " --> pdb=" O ALA J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 206 Processing helix chain 'J' and resid 217 through 221 Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.658A pdb=" N LYS J 230 " --> pdb=" O LYS J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 265 Processing helix chain 'J' and resid 281 through 292 removed outlier: 4.247A pdb=" N VAL J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 removed outlier: 3.580A pdb=" N GLY J 312 " --> pdb=" O LEU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 5 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 144 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 10 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N MET A 106 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 104 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU A 14 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 102 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 107 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE A 59 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 109 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 57 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU A 111 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 55 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 113 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASN A 53 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 14.246A pdb=" N VAL A 55 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LEU A 162 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 160 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 226 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 195 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A 223 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA A 193 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A 225 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 5.972A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) 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 214 through 216 removed outlier: 5.763A pdb=" N ASP A 214 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.804A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 102 removed outlier: 4.181A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 102 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 158 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 142 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.831A pdb=" N SER I 108 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 30 through 35 current: chain 'I' and resid 158 through 163 Processing sheet with id=AB3, first strand: chain 'I' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 99 current: chain 'I' and resid 242 through 243 Processing sheet with id=AB4, first strand: chain 'I' and resid 50 through 57 removed outlier: 4.569A pdb=" N CYS I 82 " --> pdb=" O VAL I 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 223 " --> pdb=" O CYS I 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.605A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR H 160 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 50 through 56 Processing sheet with id=AB9, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'H' and resid 260 through 262 Processing sheet with id=AC2, first strand: chain 'G' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 30 through 35 current: chain 'G' and resid 157 through 163 removed outlier: 3.521A pdb=" N THR G 160 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'G' and resid 50 through 56 removed outlier: 4.471A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.529A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AC8, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.634A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AD2, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD3, first strand: chain 'F' and resid 50 through 56 removed outlier: 4.527A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.224A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AD6, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.754A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 35 current: chain 'E' and resid 157 through 163 Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AD9, first strand: chain 'E' and resid 50 through 55 Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AE2, first strand: chain 'D' and resid 19 through 21 removed outlier: 3.752A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AE4, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.587A pdb=" N ILE D 93 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AE6, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AE7, first strand: chain 'J' and resid 301 through 304 853 hydrogen bonds defined for protein. 2286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6953 1.34 - 1.46: 5322 1.46 - 1.58: 11941 1.58 - 1.70: 202 1.70 - 1.82: 191 Bond restraints: 24609 Sorted by residual: bond pdb=" CA ARG I 146 " pdb=" C ARG I 146 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.40e-02 5.10e+03 3.31e+00 bond pdb=" O5' C C 58 " pdb=" C5' C C 58 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.06e+00 bond pdb=" CB GLU E 29 " pdb=" CG GLU E 29 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CG1 ILE J 251 " pdb=" CD1 ILE J 251 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.70e+00 bond pdb=" CA ILE I 288 " pdb=" CB ILE I 288 " ideal model delta sigma weight residual 1.537 1.553 -0.016 1.29e-02 6.01e+03 1.53e+00 ... (remaining 24604 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.51: 867 105.51 - 112.69: 12995 112.69 - 119.86: 8182 119.86 - 127.04: 11219 127.04 - 134.22: 437 Bond angle restraints: 33700 Sorted by residual: angle pdb=" CB GLU E 29 " pdb=" CG GLU E 29 " pdb=" CD GLU E 29 " ideal model delta sigma weight residual 112.60 118.74 -6.14 1.70e+00 3.46e-01 1.30e+01 angle pdb=" C ILE D 164 " pdb=" N GLU D 165 " pdb=" CA GLU D 165 " ideal model delta sigma weight residual 120.82 126.17 -5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" CB MET D 221 " pdb=" CG MET D 221 " pdb=" SD MET D 221 " ideal model delta sigma weight residual 112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N ARG I 146 " pdb=" CA ARG I 146 " pdb=" C ARG I 146 " ideal model delta sigma weight residual 112.54 108.46 4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA GLY D 218 " pdb=" C GLY D 218 " pdb=" N CYS D 219 " ideal model delta sigma weight residual 114.23 117.13 -2.90 8.80e-01 1.29e+00 1.09e+01 ... (remaining 33695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 13910 33.17 - 66.35: 907 66.35 - 99.52: 76 99.52 - 132.70: 0 132.70 - 165.87: 1 Dihedral angle restraints: 14894 sinusoidal: 6984 harmonic: 7910 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 232.00 66.13 165.87 1 1.70e+01 3.46e-03 6.54e+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 -128.00 -50.55 -77.45 1 1.70e+01 3.46e-03 2.60e+01 dihedral pdb=" CA ASP B 36 " pdb=" C ASP B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 14891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2677 0.039 - 0.077: 811 0.077 - 0.116: 176 0.116 - 0.154: 69 0.154 - 0.193: 6 Chirality restraints: 3739 Sorted by residual: chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.60 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" C3' G C 41 " pdb=" C4' G C 41 " pdb=" O3' G C 41 " pdb=" C2' G C 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" C1' A C 22 " pdb=" O4' A C 22 " pdb=" C2' A C 22 " pdb=" N9 A C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 3736 not shown) Planarity restraints: 3950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 75 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO H 76 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 273 " 0.012 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE F 273 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 273 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 273 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE F 273 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 273 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 273 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 288 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO I 289 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 289 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 289 " 0.028 5.00e-02 4.00e+02 ... (remaining 3947 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3923 2.76 - 3.29: 21305 3.29 - 3.83: 39441 3.83 - 4.36: 46178 4.36 - 4.90: 81021 Nonbonded interactions: 191868 Sorted by model distance: nonbonded pdb=" O2' G C 5 " pdb=" O PHE I 21 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 108 " pdb=" O GLY B 124 " model vdw 2.226 3.040 nonbonded pdb=" O ALA D 143 " pdb=" OG SER D 174 " model vdw 2.226 3.040 nonbonded pdb=" O2' C C 29 " pdb=" O PHE E 21 " model vdw 2.237 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 105 " model vdw 2.261 3.040 ... (remaining 191863 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 12 through 332) selection = (chain 'E' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'F' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'G' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'H' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'I' and (resid 12 through 51 or resid 79 through 332)) } 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: 3.400 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: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 64.110 Find NCS groups from input model: 0.760 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.003 0.051 24609 Z= 0.213 Angle : 0.585 10.526 33700 Z= 0.317 Chirality : 0.041 0.193 3739 Planarity : 0.004 0.067 3950 Dihedral : 19.622 165.872 9784 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.42 % Allowed : 29.07 % Favored : 70.51 % 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: -0.84 (0.16), residues: 2662 helix: 0.47 (0.18), residues: 770 sheet: 1.02 (0.27), residues: 430 loop : -1.70 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 74 HIS 0.015 0.001 HIS A 181 PHE 0.041 0.001 PHE F 273 TYR 0.016 0.001 TYR A 142 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 229 MET cc_start: 0.8355 (tpp) cc_final: 0.7945 (tpp) outliers start: 10 outliers final: 2 residues processed: 214 average time/residue: 0.3758 time to fit residues: 127.1307 Evaluate side-chains 140 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 53 ASN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24609 Z= 0.275 Angle : 0.568 8.625 33700 Z= 0.303 Chirality : 0.039 0.221 3739 Planarity : 0.004 0.061 3950 Dihedral : 16.112 159.589 4301 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.51 % Allowed : 26.64 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2662 helix: 1.16 (0.19), residues: 799 sheet: 0.88 (0.27), residues: 435 loop : -1.48 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.012 0.001 PHE H 95 TYR 0.013 0.001 TYR B 155 ARG 0.009 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 137 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 91 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8036 (tp) REVERT: H 229 MET cc_start: 0.8339 (tpp) cc_final: 0.7656 (tpp) REVERT: F 62 MET cc_start: 0.7845 (pmm) cc_final: 0.7236 (pmm) outliers start: 60 outliers final: 27 residues processed: 188 average time/residue: 0.3474 time to fit residues: 103.4410 Evaluate side-chains 149 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 250 optimal weight: 0.0270 chunk 270 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 85 optimal weight: 0.0980 chunk 200 optimal weight: 9.9990 overall best weight: 3.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN J 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24609 Z= 0.253 Angle : 0.545 8.396 33700 Z= 0.288 Chirality : 0.039 0.224 3739 Planarity : 0.004 0.057 3950 Dihedral : 16.155 159.743 4299 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.22 % Allowed : 26.06 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2662 helix: 1.44 (0.19), residues: 793 sheet: 0.82 (0.27), residues: 424 loop : -1.45 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.026 0.001 PHE J 92 TYR 0.011 0.001 TYR J 301 ARG 0.004 0.000 ARG J 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 124 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.7911 (tpt) cc_final: 0.7614 (tpp) REVERT: H 229 MET cc_start: 0.8434 (tpp) cc_final: 0.7701 (tpp) REVERT: J 46 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8877 (t) REVERT: J 104 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7907 (mtm) outliers start: 77 outliers final: 42 residues processed: 193 average time/residue: 0.3317 time to fit residues: 104.5198 Evaluate side-chains 157 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN H 178 ASN F 140 ASN J 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24609 Z= 0.336 Angle : 0.578 7.610 33700 Z= 0.304 Chirality : 0.040 0.244 3739 Planarity : 0.004 0.053 3950 Dihedral : 16.210 161.922 4299 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.68 % Allowed : 26.01 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2662 helix: 1.37 (0.19), residues: 798 sheet: 0.63 (0.27), residues: 418 loop : -1.44 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.009 0.001 HIS F 60 PHE 0.019 0.002 PHE D 200 TYR 0.012 0.001 TYR F 210 ARG 0.008 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 116 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 91 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8024 (tp) REVERT: H 229 MET cc_start: 0.8437 (tpp) cc_final: 0.7758 (tpp) REVERT: F 62 MET cc_start: 0.7745 (pmm) cc_final: 0.7181 (pmm) REVERT: D 259 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6789 (ttp80) REVERT: J 104 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8008 (mtm) outliers start: 88 outliers final: 58 residues processed: 193 average time/residue: 0.3341 time to fit residues: 104.6778 Evaluate side-chains 170 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 109 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 238 optimal weight: 0.0970 chunk 67 optimal weight: 8.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24609 Z= 0.349 Angle : 0.593 8.582 33700 Z= 0.312 Chirality : 0.040 0.249 3739 Planarity : 0.004 0.050 3950 Dihedral : 16.285 162.426 4299 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.48 % Allowed : 25.35 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2662 helix: 1.27 (0.19), residues: 801 sheet: 0.33 (0.27), residues: 419 loop : -1.42 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.021 0.002 PHE J 92 TYR 0.019 0.001 TYR A 62 ARG 0.006 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 111 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 328 MET cc_start: 0.7743 (mtm) cc_final: 0.7343 (mtm) REVERT: H 91 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8053 (tp) REVERT: H 229 MET cc_start: 0.8432 (tpp) cc_final: 0.7732 (tpp) REVERT: F 62 MET cc_start: 0.7703 (pmm) cc_final: 0.7184 (pmm) REVERT: D 106 MET cc_start: 0.7349 (tmm) cc_final: 0.7072 (tmm) REVERT: D 259 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6803 (ttp80) REVERT: D 301 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8651 (tp) REVERT: J 46 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8875 (t) REVERT: J 104 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7987 (mtm) REVERT: J 135 MET cc_start: 0.8338 (tmm) cc_final: 0.7941 (ppp) outliers start: 107 outliers final: 67 residues processed: 206 average time/residue: 0.3492 time to fit residues: 114.9783 Evaluate side-chains 178 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 106 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 266 optimal weight: 0.0670 chunk 220 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 0.0970 overall best weight: 2.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24609 Z= 0.185 Angle : 0.548 9.124 33700 Z= 0.284 Chirality : 0.039 0.242 3739 Planarity : 0.004 0.047 3950 Dihedral : 16.269 160.775 4299 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.39 % Allowed : 26.10 % Favored : 70.51 % 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: -0.23 (0.17), residues: 2662 helix: 1.44 (0.19), residues: 800 sheet: 0.58 (0.27), residues: 432 loop : -1.38 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 264 HIS 0.007 0.001 HIS J 116 PHE 0.023 0.001 PHE J 92 TYR 0.013 0.001 TYR A 62 ARG 0.011 0.000 ARG H 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 114 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 91 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7991 (tp) REVERT: H 229 MET cc_start: 0.8423 (tpp) cc_final: 0.7663 (tpp) REVERT: F 62 MET cc_start: 0.7810 (pmm) cc_final: 0.7409 (pmm) REVERT: D 106 MET cc_start: 0.7308 (tmm) cc_final: 0.7095 (tmm) REVERT: D 259 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6840 (ttp80) REVERT: D 301 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8557 (tp) REVERT: J 27 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8189 (mm) REVERT: J 46 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8864 (t) REVERT: J 104 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: J 135 MET cc_start: 0.8248 (tmm) cc_final: 0.7888 (ppp) outliers start: 81 outliers final: 49 residues processed: 184 average time/residue: 0.3206 time to fit residues: 96.6747 Evaluate side-chains 164 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 109 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 113 ASN Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 151 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24609 Z= 0.316 Angle : 0.592 11.405 33700 Z= 0.306 Chirality : 0.040 0.242 3739 Planarity : 0.004 0.046 3950 Dihedral : 16.317 163.166 4299 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.55 % Allowed : 25.55 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2662 helix: 1.36 (0.19), residues: 800 sheet: 0.43 (0.27), residues: 425 loop : -1.40 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.006 0.001 HIS B 120 PHE 0.022 0.001 PHE J 92 TYR 0.012 0.001 TYR F 210 ARG 0.006 0.000 ARG H 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 111 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 328 MET cc_start: 0.7707 (mtm) cc_final: 0.7265 (mtm) REVERT: H 91 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8035 (tp) REVERT: H 229 MET cc_start: 0.8441 (tpp) cc_final: 0.7745 (tpp) REVERT: F 62 MET cc_start: 0.7858 (pmm) cc_final: 0.7531 (pmm) REVERT: D 259 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6730 (ttp80) REVERT: D 301 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8597 (tp) REVERT: J 104 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: J 135 MET cc_start: 0.8346 (tmm) cc_final: 0.7981 (ppp) outliers start: 85 outliers final: 69 residues processed: 184 average time/residue: 0.3359 time to fit residues: 101.8416 Evaluate side-chains 182 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 109 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 113 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24609 Z= 0.230 Angle : 0.568 12.601 33700 Z= 0.293 Chirality : 0.039 0.241 3739 Planarity : 0.004 0.045 3950 Dihedral : 16.322 162.064 4299 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.60 % Allowed : 25.55 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2662 helix: 1.39 (0.19), residues: 801 sheet: 0.50 (0.27), residues: 429 loop : -1.37 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 264 HIS 0.007 0.001 HIS B 120 PHE 0.020 0.001 PHE J 92 TYR 0.010 0.001 TYR B 155 ARG 0.007 0.000 ARG H 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 115 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.7884 (tpt) cc_final: 0.7590 (tpt) REVERT: I 328 MET cc_start: 0.7686 (mtm) cc_final: 0.7229 (mtm) REVERT: H 91 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7985 (tp) REVERT: H 229 MET cc_start: 0.8416 (tpp) cc_final: 0.7687 (tpp) REVERT: D 259 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6817 (ttp80) REVERT: D 301 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8584 (tp) outliers start: 86 outliers final: 72 residues processed: 190 average time/residue: 0.3224 time to fit residues: 100.0015 Evaluate side-chains 186 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 111 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 113 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 223 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN F 140 ASN J 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24609 Z= 0.161 Angle : 0.569 13.052 33700 Z= 0.288 Chirality : 0.039 0.236 3739 Planarity : 0.004 0.045 3950 Dihedral : 16.333 161.046 4299 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.93 % Allowed : 26.10 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2662 helix: 1.47 (0.19), residues: 801 sheet: 0.65 (0.27), residues: 441 loop : -1.32 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 74 HIS 0.017 0.001 HIS F 60 PHE 0.010 0.001 PHE E 273 TYR 0.010 0.001 TYR B 155 ARG 0.010 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 120 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 328 MET cc_start: 0.7600 (mtm) cc_final: 0.7124 (mtm) REVERT: H 91 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7969 (tp) REVERT: H 229 MET cc_start: 0.8428 (tpp) cc_final: 0.7627 (tpp) REVERT: D 259 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6824 (ttp80) REVERT: D 301 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8544 (tp) REVERT: J 121 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9193 (mm) outliers start: 70 outliers final: 57 residues processed: 181 average time/residue: 0.3248 time to fit residues: 96.5562 Evaluate side-chains 174 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 113 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.0020 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 273 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 133 optimal weight: 0.0970 chunk 173 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24609 Z= 0.145 Angle : 0.584 13.150 33700 Z= 0.294 Chirality : 0.039 0.277 3739 Planarity : 0.004 0.047 3950 Dihedral : 16.324 160.597 4299 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.09 % Allowed : 27.23 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2662 helix: 1.50 (0.19), residues: 798 sheet: 0.69 (0.27), residues: 441 loop : -1.30 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 74 HIS 0.015 0.001 HIS F 60 PHE 0.010 0.001 PHE G 273 TYR 0.010 0.001 TYR B 155 ARG 0.011 0.000 ARG A 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.8060 (tpt) cc_final: 0.7811 (tpt) REVERT: I 328 MET cc_start: 0.7575 (mtm) cc_final: 0.7090 (mtm) REVERT: H 229 MET cc_start: 0.8397 (tpp) cc_final: 0.7572 (tpp) REVERT: F 328 MET cc_start: 0.6787 (tpp) cc_final: 0.6201 (mmt) REVERT: D 259 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6779 (ttp80) REVERT: D 301 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8537 (tp) REVERT: J 121 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9200 (mm) outliers start: 50 outliers final: 44 residues processed: 162 average time/residue: 0.3559 time to fit residues: 93.8723 Evaluate side-chains 162 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.046977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032131 restraints weight = 117014.061| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 4.21 r_work: 0.2436 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 24609 Z= 0.172 Angle : 0.714 59.199 33700 Z= 0.387 Chirality : 0.040 0.441 3739 Planarity : 0.004 0.048 3950 Dihedral : 16.323 160.596 4299 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.13 % Allowed : 27.10 % Favored : 70.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2662 helix: 1.47 (0.19), residues: 800 sheet: 0.69 (0.27), residues: 441 loop : -1.29 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 74 HIS 0.014 0.001 HIS F 60 PHE 0.010 0.001 PHE G 273 TYR 0.010 0.001 TYR B 155 ARG 0.010 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.19 seconds wall clock time: 79 minutes 5.66 seconds (4745.66 seconds total)