Starting phenix.real_space_refine on Fri Jun 20 09:07:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_39167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_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/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_39167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_39167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_39167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ydb_39167/06_2025/8ydb_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. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.51, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 6.24 Conformation dependent library (CDL) restraints added in 2.7 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: 9.36 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: 8.74 Time building geometry restraints manager: 7.10 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: 0.00 - 2.11: 33231 2.11 - 4.21: 417 4.21 - 6.32: 42 6.32 - 8.42: 3 8.42 - 10.53: 7 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 60.770 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.630 ------------------------------------------------------------------------------- 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= 0.151 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 Details of bonding type rmsd hydrogen bonds : bond 0.17420 ( 867) hydrogen bonds : angle 5.99629 ( 2446) covalent geometry : bond 0.00330 (24609) covalent geometry : angle 0.58476 (33700) *********************** 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 to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 2.588 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: 0.3549 time to fit residues: 119.8929 Evaluate side-chains 140 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 2.530 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032206 restraints weight = 117350.792| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.31 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 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= 0.198 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 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 867) hydrogen bonds : angle 4.63647 ( 2446) covalent geometry : bond 0.00428 (24609) covalent geometry : angle 0.56825 (33700) *********************** 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 to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9306 (mpp80) cc_final: 0.8943 (mpp80) REVERT: A 163 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8481 (mmm-85) REVERT: A 249 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9335 (mm) REVERT: B 71 LEU cc_start: 0.9394 (mt) cc_final: 0.9129 (mt) REVERT: B 83 TYR cc_start: 0.9110 (m-80) cc_final: 0.8803 (m-80) REVERT: B 115 MET cc_start: 0.9292 (tpt) cc_final: 0.8675 (tpt) REVERT: H 91 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8804 (tp) REVERT: H 229 MET cc_start: 0.9131 (tpp) cc_final: 0.7645 (tpp) REVERT: G 120 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8328 (tm-30) REVERT: G 249 MET cc_start: 0.9081 (mtp) cc_final: 0.8794 (ttm) REVERT: F 62 MET cc_start: 0.7352 (pmm) cc_final: 0.6639 (pmm) REVERT: F 120 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8571 (tm-30) REVERT: E 313 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8763 (tp) REVERT: D 221 MET cc_start: 0.7709 (mmm) cc_final: 0.7392 (mmm) REVERT: J 62 MET cc_start: 0.8053 (mpt) cc_final: 0.7833 (mmt) REVERT: J 138 MET cc_start: 0.8226 (ppp) cc_final: 0.7532 (ppp) outliers start: 60 outliers final: 27 residues processed: 188 average time/residue: 0.3610 time to fit residues: 108.0150 Evaluate side-chains 151 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 A residue 249 LEU 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 E residue 313 ILE 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 248 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 29 HIS ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN D 140 ASN J 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.030731 restraints weight = 120834.573| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 4.13 r_work: 0.2356 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 24609 Z= 0.325 Angle : 0.651 7.703 33700 Z= 0.344 Chirality : 0.041 0.230 3739 Planarity : 0.004 0.062 3950 Dihedral : 16.300 162.858 4299 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.56 % Allowed : 25.14 % 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: -0.53 (0.16), residues: 2662 helix: 1.14 (0.19), residues: 799 sheet: 0.35 (0.27), residues: 423 loop : -1.50 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.024 0.002 PHE J 92 TYR 0.016 0.002 TYR F 169 ARG 0.004 0.001 ARG J 88 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 867) hydrogen bonds : angle 4.75429 ( 2446) covalent geometry : bond 0.00701 (24609) covalent geometry : angle 0.65089 (33700) *********************** 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 227 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 118 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: A 249 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9346 (mm) REVERT: B 71 LEU cc_start: 0.9449 (mt) cc_final: 0.9178 (mt) REVERT: B 83 TYR cc_start: 0.9173 (m-80) cc_final: 0.8856 (m-80) REVERT: B 115 MET cc_start: 0.9099 (tpt) cc_final: 0.8539 (tpt) REVERT: I 106 MET cc_start: 0.9299 (ttp) cc_final: 0.8764 (tmm) REVERT: H 91 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8956 (tp) REVERT: H 204 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8912 (ttm110) REVERT: H 229 MET cc_start: 0.9433 (tpp) cc_final: 0.8021 (tpp) REVERT: G 120 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8675 (tm-30) REVERT: G 236 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9080 (mmtt) REVERT: G 304 MET cc_start: 0.9497 (ttt) cc_final: 0.9239 (tmm) REVERT: F 120 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8942 (tm-30) REVERT: F 221 MET cc_start: 0.9243 (mmt) cc_final: 0.9039 (mmm) REVERT: D 221 MET cc_start: 0.8217 (mmm) cc_final: 0.7939 (mmm) REVERT: D 259 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7495 (ttp80) REVERT: D 301 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9284 (tp) REVERT: J 46 THR cc_start: 0.9746 (OUTLIER) cc_final: 0.9396 (t) REVERT: J 62 MET cc_start: 0.8285 (mpt) cc_final: 0.8026 (mmt) REVERT: J 104 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8367 (mtm) REVERT: J 135 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (tmm) REVERT: J 138 MET cc_start: 0.8677 (ppp) cc_final: 0.8360 (ppp) outliers start: 109 outliers final: 59 residues processed: 217 average time/residue: 0.3409 time to fit residues: 118.1219 Evaluate side-chains 177 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 109 time to evaluate : 2.711 ------------------------------------------------------------------------------- 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 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 249 LEU 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 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 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 204 ARG 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 236 LYS 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 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 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 113 ASN 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 267 ASP Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 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 104 MET Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 135 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 88 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN H 120 GLN F 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.031476 restraints weight = 119243.502| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.26 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24609 Z= 0.129 Angle : 0.528 10.337 33700 Z= 0.278 Chirality : 0.039 0.236 3739 Planarity : 0.004 0.052 3950 Dihedral : 16.244 159.569 4299 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.59 % Allowed : 26.56 % 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: -0.26 (0.17), residues: 2662 helix: 1.44 (0.19), residues: 799 sheet: 0.63 (0.27), residues: 423 loop : -1.43 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 264 HIS 0.007 0.001 HIS J 116 PHE 0.020 0.001 PHE D 200 TYR 0.024 0.001 TYR G 169 ARG 0.009 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 867) hydrogen bonds : angle 4.32127 ( 2446) covalent geometry : bond 0.00281 (24609) covalent geometry : angle 0.52830 (33700) *********************** 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 183 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7601 (mmm160) REVERT: A 73 GLN cc_start: 0.9014 (pm20) cc_final: 0.8556 (pm20) REVERT: A 249 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9318 (mm) REVERT: B 71 LEU cc_start: 0.9453 (mt) cc_final: 0.9195 (mt) REVERT: B 115 MET cc_start: 0.9053 (tpt) cc_final: 0.8585 (tpt) REVERT: I 70 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: I 106 MET cc_start: 0.9072 (ttp) cc_final: 0.8627 (tmm) REVERT: I 304 MET cc_start: 0.9481 (ttm) cc_final: 0.9114 (tmm) REVERT: H 229 MET cc_start: 0.9135 (tpp) cc_final: 0.7577 (tpp) REVERT: G 120 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 236 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9125 (mmtt) REVERT: F 62 MET cc_start: 0.7326 (pmm) cc_final: 0.6577 (pmm) REVERT: F 120 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8665 (tm-30) REVERT: E 229 MET cc_start: 0.8937 (mmp) cc_final: 0.8683 (mmp) REVERT: D 221 MET cc_start: 0.7947 (mmm) cc_final: 0.7669 (mmm) REVERT: J 46 THR cc_start: 0.9749 (OUTLIER) cc_final: 0.9361 (t) REVERT: J 104 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: J 135 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: J 138 MET cc_start: 0.8382 (ppp) cc_final: 0.8129 (ppp) outliers start: 62 outliers final: 35 residues processed: 175 average time/residue: 0.3400 time to fit residues: 97.0503 Evaluate side-chains 156 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 2.804 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 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 236 LYS 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 267 ASP Chi-restraints excluded: chain E residue 91 LEU 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 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 233 ASP 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 135 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 Chi-restraints excluded: chain J residue 292 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.030914 restraints weight = 119266.875| |-----------------------------------------------------------------------------| r_work (start): 0.2537 rms_B_bonded: 4.19 r_work: 0.2381 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24609 Z= 0.207 Angle : 0.562 10.722 33700 Z= 0.293 Chirality : 0.039 0.244 3739 Planarity : 0.004 0.049 3950 Dihedral : 16.257 161.992 4299 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.68 % Allowed : 25.55 % Favored : 70.77 % 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: -0.29 (0.17), residues: 2662 helix: 1.45 (0.19), residues: 799 sheet: 0.42 (0.27), residues: 424 loop : -1.40 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.020 0.001 PHE J 92 TYR 0.017 0.001 TYR G 169 ARG 0.006 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 867) hydrogen bonds : angle 4.36498 ( 2446) covalent geometry : bond 0.00452 (24609) covalent geometry : angle 0.56191 (33700) *********************** 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 203 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 115 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7902 (mmm160) REVERT: A 73 GLN cc_start: 0.9126 (pm20) cc_final: 0.8749 (pm20) REVERT: A 249 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9341 (mm) REVERT: B 71 LEU cc_start: 0.9433 (mt) cc_final: 0.9168 (mt) REVERT: B 115 MET cc_start: 0.9079 (tpt) cc_final: 0.8583 (tpt) REVERT: I 70 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8889 (mp0) REVERT: I 106 MET cc_start: 0.9266 (ttp) cc_final: 0.8786 (tmm) REVERT: H 91 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8934 (tp) REVERT: H 229 MET cc_start: 0.9400 (tpp) cc_final: 0.7942 (tpp) REVERT: G 36 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8201 (p0) REVERT: G 120 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8575 (tm-30) REVERT: G 236 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9114 (mmtt) REVERT: F 62 MET cc_start: 0.7295 (pmm) cc_final: 0.6605 (pmm) REVERT: F 120 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8948 (tm-30) REVERT: E 229 MET cc_start: 0.9183 (mmp) cc_final: 0.8874 (mmp) REVERT: D 221 MET cc_start: 0.8242 (mmm) cc_final: 0.7934 (mmm) REVERT: D 229 MET cc_start: 0.7612 (ttt) cc_final: 0.7196 (ttp) REVERT: D 259 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7547 (ttp80) REVERT: D 300 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 104 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: J 135 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8175 (tmm) REVERT: J 233 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9257 (pp) REVERT: J 322 MET cc_start: 0.8707 (tpp) cc_final: 0.8363 (tpp) outliers start: 88 outliers final: 56 residues processed: 191 average time/residue: 0.3769 time to fit residues: 117.0803 Evaluate side-chains 180 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 114 time to evaluate : 2.855 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU 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 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 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 G residue 27 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS 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 140 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 47 LEU 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 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 275 ILE Chi-restraints excluded: chain D residue 300 LEU 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 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 233 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 320 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 183 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 264 optimal weight: 0.0270 overall best weight: 2.9844 ------------------------------------------------------------------------------- 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** F 140 ASN ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.031218 restraints weight = 118049.191| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 4.19 r_work: 0.2394 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24609 Z= 0.156 Angle : 0.536 11.386 33700 Z= 0.280 Chirality : 0.039 0.241 3739 Planarity : 0.004 0.047 3950 Dihedral : 16.257 161.527 4299 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.43 % Allowed : 25.76 % Favored : 70.81 % 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: -0.22 (0.17), residues: 2662 helix: 1.50 (0.19), residues: 799 sheet: 0.52 (0.27), residues: 442 loop : -1.40 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 PHE 0.023 0.001 PHE J 92 TYR 0.015 0.001 TYR G 169 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 867) hydrogen bonds : angle 4.26586 ( 2446) covalent geometry : bond 0.00341 (24609) covalent geometry : angle 0.53584 (33700) *********************** 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 200 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 118 time to evaluate : 4.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9140 (pm20) cc_final: 0.8791 (pm20) REVERT: A 249 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9334 (mm) REVERT: B 71 LEU cc_start: 0.9436 (mt) cc_final: 0.9164 (mt) REVERT: B 115 MET cc_start: 0.9111 (tpt) cc_final: 0.8649 (tpt) REVERT: B 134 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9036 (mttt) REVERT: I 70 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: I 304 MET cc_start: 0.9671 (ttm) cc_final: 0.9220 (tmm) REVERT: H 229 MET cc_start: 0.9375 (tpp) cc_final: 0.7906 (tpp) REVERT: H 304 MET cc_start: 0.9540 (tmm) cc_final: 0.9078 (tmm) REVERT: G 120 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 304 MET cc_start: 0.9494 (tmm) cc_final: 0.9139 (tmm) REVERT: F 62 MET cc_start: 0.7336 (pmm) cc_final: 0.6736 (pmm) REVERT: F 120 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8926 (tm-30) REVERT: E 229 MET cc_start: 0.9109 (mmp) cc_final: 0.8785 (mmp) REVERT: D 106 MET cc_start: 0.8555 (tmm) cc_final: 0.7939 (tmm) REVERT: D 221 MET cc_start: 0.8233 (mmm) cc_final: 0.7911 (mmm) REVERT: D 259 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7506 (ttp80) REVERT: J 104 MET cc_start: 0.8665 (mtt) cc_final: 0.8333 (mtm) REVERT: J 135 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (tmm) REVERT: J 322 MET cc_start: 0.8778 (tpp) cc_final: 0.8317 (tpp) outliers start: 82 outliers final: 58 residues processed: 189 average time/residue: 0.3950 time to fit residues: 121.5980 Evaluate side-chains 177 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 114 time to evaluate : 2.912 ------------------------------------------------------------------------------- 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 249 LEU 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 123 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 142 ILE 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 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 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 223 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 91 LEU 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 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 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 MET 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 Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 201 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.030762 restraints weight = 119595.464| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 4.19 r_work: 0.2377 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24609 Z= 0.198 Angle : 0.565 10.761 33700 Z= 0.292 Chirality : 0.039 0.238 3739 Planarity : 0.004 0.047 3950 Dihedral : 16.294 162.975 4299 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.89 % Allowed : 25.39 % 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: -0.25 (0.17), residues: 2662 helix: 1.46 (0.19), residues: 799 sheet: 0.42 (0.27), residues: 438 loop : -1.38 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 33 HIS 0.004 0.001 HIS F 60 PHE 0.021 0.001 PHE J 92 TYR 0.014 0.001 TYR G 169 ARG 0.004 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 867) hydrogen bonds : angle 4.33889 ( 2446) covalent geometry : bond 0.00432 (24609) covalent geometry : angle 0.56462 (33700) *********************** 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 209 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 116 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9136 (pm20) cc_final: 0.8819 (pm20) REVERT: A 163 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8529 (mmt90) REVERT: A 249 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9344 (mm) REVERT: B 71 LEU cc_start: 0.9441 (mt) cc_final: 0.9167 (mt) REVERT: B 115 MET cc_start: 0.9077 (tpt) cc_final: 0.8595 (tpt) REVERT: B 134 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8963 (mttt) REVERT: I 70 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: I 106 MET cc_start: 0.9223 (ttp) cc_final: 0.8695 (tmm) REVERT: I 304 MET cc_start: 0.9681 (ttm) cc_final: 0.9228 (tmm) REVERT: H 91 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8916 (tp) REVERT: H 229 MET cc_start: 0.9400 (tpp) cc_final: 0.7963 (tpp) REVERT: H 304 MET cc_start: 0.9565 (tmm) cc_final: 0.9075 (tmm) REVERT: G 36 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8123 (p0) REVERT: G 120 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8550 (tm-30) REVERT: G 236 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9143 (mmtt) REVERT: F 62 MET cc_start: 0.7314 (pmm) cc_final: 0.6717 (pmm) REVERT: F 120 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8938 (tm-30) REVERT: F 253 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9065 (tptp) REVERT: E 229 MET cc_start: 0.9066 (mmt) cc_final: 0.8866 (mmp) REVERT: D 221 MET cc_start: 0.8288 (mmm) cc_final: 0.7957 (mmm) REVERT: D 259 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: J 104 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: J 135 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (tmm) REVERT: J 138 MET cc_start: 0.8341 (ppp) cc_final: 0.7779 (ppp) REVERT: J 322 MET cc_start: 0.8905 (tpp) cc_final: 0.8417 (tpp) outliers start: 93 outliers final: 69 residues processed: 197 average time/residue: 0.3403 time to fit residues: 108.6713 Evaluate side-chains 192 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 113 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU 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 98 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 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 142 ILE 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 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS 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 38 LEU Chi-restraints excluded: chain F residue 113 ASN 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 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 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 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 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 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 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 216 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 161 optimal weight: 0.0170 chunk 243 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- 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 106 HIS ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.045496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.031036 restraints weight = 119801.627| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 4.09 r_work: 0.2376 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24609 Z= 0.223 Angle : 0.585 11.859 33700 Z= 0.302 Chirality : 0.040 0.244 3739 Planarity : 0.004 0.045 3950 Dihedral : 16.336 163.156 4299 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.89 % Allowed : 25.47 % Favored : 70.64 % 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: -0.31 (0.17), residues: 2662 helix: 1.39 (0.19), residues: 801 sheet: 0.37 (0.27), residues: 425 loop : -1.38 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.004 0.001 HIS F 60 PHE 0.019 0.001 PHE J 92 TYR 0.013 0.001 TYR G 169 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 867) hydrogen bonds : angle 4.39574 ( 2446) covalent geometry : bond 0.00484 (24609) covalent geometry : angle 0.58461 (33700) *********************** 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 207 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 114 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9143 (pm20) cc_final: 0.8829 (pm20) REVERT: A 163 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8591 (mmt90) REVERT: A 249 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9346 (mm) REVERT: B 71 LEU cc_start: 0.9447 (mt) cc_final: 0.9170 (mt) REVERT: B 115 MET cc_start: 0.9077 (tpt) cc_final: 0.8599 (tpt) REVERT: B 134 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8944 (mttt) REVERT: I 70 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8922 (mp0) REVERT: I 106 MET cc_start: 0.9219 (ttp) cc_final: 0.8714 (tmm) REVERT: I 304 MET cc_start: 0.9677 (ttm) cc_final: 0.9226 (tmm) REVERT: H 91 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8953 (tp) REVERT: H 229 MET cc_start: 0.9403 (tpp) cc_final: 0.7986 (tpp) REVERT: H 304 MET cc_start: 0.9592 (tmm) cc_final: 0.9084 (tmm) REVERT: G 36 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8134 (p0) REVERT: G 120 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8554 (tm-30) REVERT: G 236 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9154 (mmtt) REVERT: G 304 MET cc_start: 0.9541 (tmm) cc_final: 0.9140 (tmm) REVERT: F 62 MET cc_start: 0.7411 (pmm) cc_final: 0.6910 (pmm) REVERT: F 120 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8926 (tm-30) REVERT: F 253 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9089 (tptp) REVERT: D 221 MET cc_start: 0.8276 (mmm) cc_final: 0.7874 (mmm) REVERT: D 229 MET cc_start: 0.7448 (ttt) cc_final: 0.7102 (ttp) REVERT: D 259 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: D 301 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9286 (tp) REVERT: J 135 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (tmm) REVERT: J 138 MET cc_start: 0.8439 (ppp) cc_final: 0.7969 (ppp) REVERT: J 322 MET cc_start: 0.8916 (tpp) cc_final: 0.8414 (tpp) outliers start: 93 outliers final: 71 residues processed: 196 average time/residue: 0.3996 time to fit residues: 126.4616 Evaluate side-chains 193 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 112 time to evaluate : 2.771 ------------------------------------------------------------------------------- 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 112 VAL 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 249 LEU 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 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 329 PHE 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 142 ILE 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 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS 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 38 LEU Chi-restraints excluded: chain F residue 113 ASN Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 253 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 81 SER 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 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 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 Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 182 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 117 optimal weight: 0.0470 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 overall best weight: 5.6086 ------------------------------------------------------------------------------- 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 F 317 HIS J 106 HIS ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.031028 restraints weight = 121147.062| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 4.08 r_work: 0.2386 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24609 Z= 0.269 Angle : 0.623 11.661 33700 Z= 0.322 Chirality : 0.040 0.250 3739 Planarity : 0.004 0.045 3950 Dihedral : 16.429 164.034 4299 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.06 % Allowed : 25.30 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2662 helix: 1.27 (0.19), residues: 798 sheet: 0.23 (0.27), residues: 430 loop : -1.42 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS F 60 PHE 0.019 0.002 PHE F 329 TYR 0.013 0.001 TYR F 210 ARG 0.005 0.000 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 867) hydrogen bonds : angle 4.52089 ( 2446) covalent geometry : bond 0.00584 (24609) covalent geometry : angle 0.62292 (33700) *********************** 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 211 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 114 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.7977 (mmm160) REVERT: A 163 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8708 (mmt90) REVERT: A 249 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9371 (mm) REVERT: B 71 LEU cc_start: 0.9463 (mt) cc_final: 0.9195 (mt) REVERT: B 72 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8985 (t) REVERT: B 115 MET cc_start: 0.9061 (tpt) cc_final: 0.8546 (tpt) REVERT: B 134 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8896 (mttt) REVERT: I 70 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: I 106 MET cc_start: 0.9220 (ttp) cc_final: 0.8721 (tmm) REVERT: I 238 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8844 (ttmt) REVERT: I 304 MET cc_start: 0.9683 (ttm) cc_final: 0.9224 (tmm) REVERT: H 91 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8975 (tp) REVERT: H 229 MET cc_start: 0.9394 (tpp) cc_final: 0.7981 (tpp) REVERT: H 304 MET cc_start: 0.9640 (tmm) cc_final: 0.9302 (tmm) REVERT: G 36 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8166 (p0) REVERT: G 120 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 236 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9135 (mmtt) REVERT: F 62 MET cc_start: 0.7443 (pmm) cc_final: 0.7009 (pmm) REVERT: F 120 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8928 (tm-30) REVERT: F 253 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9139 (tptp) REVERT: D 221 MET cc_start: 0.8325 (mmm) cc_final: 0.7927 (mmm) REVERT: D 259 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7464 (ttp80) REVERT: D 301 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9296 (tp) REVERT: J 104 MET cc_start: 0.8942 (mtm) cc_final: 0.8684 (mpp) REVERT: J 135 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: J 138 MET cc_start: 0.8531 (ppp) cc_final: 0.8089 (ppp) REVERT: J 322 MET cc_start: 0.8958 (tpp) cc_final: 0.8456 (tpp) outliers start: 97 outliers final: 72 residues processed: 201 average time/residue: 0.3928 time to fit residues: 125.7189 Evaluate side-chains 195 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 111 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU 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 72 CYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 329 PHE 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 142 ILE 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 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS 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 140 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 253 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 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain D residue 20 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 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 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 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 23 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 106 HIS ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.031073 restraints weight = 120507.082| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 4.08 r_work: 0.2387 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24609 Z= 0.245 Angle : 0.615 11.893 33700 Z= 0.316 Chirality : 0.040 0.291 3739 Planarity : 0.004 0.047 3950 Dihedral : 16.460 163.596 4299 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.81 % Allowed : 25.55 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2662 helix: 1.26 (0.19), residues: 798 sheet: 0.23 (0.27), residues: 428 loop : -1.40 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.003 0.001 HIS F 60 PHE 0.017 0.001 PHE F 329 TYR 0.014 0.001 TYR G 169 ARG 0.006 0.000 ARG J 265 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 867) hydrogen bonds : angle 4.50091 ( 2446) covalent geometry : bond 0.00533 (24609) covalent geometry : angle 0.61483 (33700) ********************** 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 207 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 116 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: A 73 GLN cc_start: 0.9359 (pm20) cc_final: 0.8726 (pm20) REVERT: A 163 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8681 (mmt90) REVERT: A 249 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9342 (mm) REVERT: B 71 LEU cc_start: 0.9468 (mt) cc_final: 0.9195 (mt) REVERT: B 72 CYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9012 (t) REVERT: B 115 MET cc_start: 0.9048 (tpt) cc_final: 0.8515 (tpt) REVERT: B 134 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8855 (mttt) REVERT: I 70 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: I 106 MET cc_start: 0.9211 (ttp) cc_final: 0.8704 (tmm) REVERT: I 238 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8848 (ttmt) REVERT: I 304 MET cc_start: 0.9683 (ttm) cc_final: 0.9213 (tmm) REVERT: H 72 MET cc_start: 0.8856 (mmt) cc_final: 0.8317 (mmt) REVERT: H 91 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8970 (tp) REVERT: H 229 MET cc_start: 0.9374 (tpp) cc_final: 0.7965 (tpp) REVERT: H 304 MET cc_start: 0.9646 (tmm) cc_final: 0.9152 (tmm) REVERT: G 36 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8122 (p0) REVERT: G 120 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8564 (tm-30) REVERT: G 236 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9115 (mmtt) REVERT: F 62 MET cc_start: 0.7436 (pmm) cc_final: 0.6984 (pmm) REVERT: F 120 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8926 (tm-30) REVERT: F 253 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9119 (tptp) REVERT: D 221 MET cc_start: 0.8314 (mmm) cc_final: 0.7891 (mmm) REVERT: D 259 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7513 (ttp80) REVERT: D 301 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9294 (tp) REVERT: J 104 MET cc_start: 0.8951 (mtm) cc_final: 0.8690 (mpp) REVERT: J 121 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9036 (mm) REVERT: J 135 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7999 (tmm) REVERT: J 138 MET cc_start: 0.8502 (ppp) cc_final: 0.8142 (ppp) REVERT: J 322 MET cc_start: 0.8985 (tpp) cc_final: 0.8472 (tpp) outliers start: 91 outliers final: 73 residues processed: 197 average time/residue: 0.4012 time to fit residues: 126.3253 Evaluate side-chains 199 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 113 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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 149 ASP 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 249 LEU 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 72 CYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU 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 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 329 PHE 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 120 GLN 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 G residue 27 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS 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 140 ASN 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 F residue 296 SER Chi-restraints excluded: chain F residue 320 MET 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 296 SER Chi-restraints excluded: chain D residue 20 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 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 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 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 160 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.031067 restraints weight = 119281.352| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 4.09 r_work: 0.2380 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24609 Z= 0.169 Angle : 0.586 11.808 33700 Z= 0.301 Chirality : 0.040 0.298 3739 Planarity : 0.004 0.052 3950 Dihedral : 16.466 162.717 4299 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.35 % Allowed : 26.01 % Favored : 70.64 % 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: -0.32 (0.17), residues: 2662 helix: 1.37 (0.19), residues: 798 sheet: 0.28 (0.27), residues: 430 loop : -1.35 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 264 HIS 0.003 0.001 HIS F 60 PHE 0.019 0.001 PHE H 329 TYR 0.014 0.001 TYR G 169 ARG 0.014 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 867) hydrogen bonds : angle 4.35656 ( 2446) covalent geometry : bond 0.00372 (24609) covalent geometry : angle 0.58611 (33700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12238.54 seconds wall clock time: 214 minutes 28.08 seconds (12868.08 seconds total)