Starting phenix.real_space_refine on Mon Mar 11 15:46:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/03_2024/6jbh_9790.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5654 2.51 5 N 1408 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8592 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2075 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "B" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2075 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "C" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2221 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "D" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2221 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Time building chain proxies: 5.31, per 1000 atoms: 0.62 Number of scatterers: 8592 At special positions: 0 Unit cell: (93.84, 88.4, 107.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1486 8.00 N 1408 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.8 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 57.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 64 through 71 removed outlier: 3.667A pdb=" N ILE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.670A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 132 removed outlier: 4.060A pdb=" N ILE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 removed outlier: 3.575A pdb=" N ILE A 137 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 138 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.871A pdb=" N SER A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.535A pdb=" N ASP A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.530A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 71 removed outlier: 3.667A pdb=" N ILE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.670A pdb=" N GLU B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 123 through 132 removed outlier: 4.060A pdb=" N ILE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.575A pdb=" N ILE B 137 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.871A pdb=" N SER B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.535A pdb=" N ASP B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.530A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.826A pdb=" N VAL C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.530A pdb=" N GLU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.993A pdb=" N ILE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 3.707A pdb=" N ALA C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.745A pdb=" N ALA C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 removed outlier: 4.204A pdb=" N TRP C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 82 " --> pdb=" O MET C 78 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 99 through 104 removed outlier: 4.003A pdb=" N GLN C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.534A pdb=" N VAL C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 removed outlier: 3.672A pdb=" N ILE C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 149 through 167 removed outlier: 4.070A pdb=" N LEU C 156 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU C 165 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 3.592A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.653A pdb=" N SER C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG C 186 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.909A pdb=" N ILE C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 235 through 259 removed outlier: 4.050A pdb=" N VAL C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 247 " --> pdb=" O TRP C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.826A pdb=" N VAL D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 21 through 30 removed outlier: 4.530A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.993A pdb=" N ILE D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Proline residue: D 44 - end of helix removed outlier: 3.707A pdb=" N ALA D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.745A pdb=" N ALA D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 removed outlier: 4.205A pdb=" N TRP D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 82 " --> pdb=" O MET D 78 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.011A pdb=" N GLN D 104 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.534A pdb=" N VAL D 111 " --> pdb=" O PRO D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 removed outlier: 3.672A pdb=" N ILE D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 149 through 167 removed outlier: 4.070A pdb=" N LEU D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 157 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 175 removed outlier: 3.592A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.653A pdb=" N SER D 183 " --> pdb=" O MET D 179 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 removed outlier: 3.908A pdb=" N ILE D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 235 through 259 removed outlier: 4.050A pdb=" N VAL D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 45 removed outlier: 5.746A pdb=" N ARG A 41 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS A 12 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE A 45 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU A 8 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN A 9 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR A 80 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 78 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.270A pdb=" N VAL A 52 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU A 214 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 54 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 216 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 213 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR A 224 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP A 215 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 45 removed outlier: 5.746A pdb=" N ARG B 41 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 12 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE B 45 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU B 8 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 9 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR B 80 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 78 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.271A pdb=" N VAL B 52 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 214 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY B 54 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU B 216 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 213 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR B 224 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP B 215 " --> pdb=" O ARG B 222 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2459 1.33 - 1.45: 1542 1.45 - 1.57: 4719 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8802 Sorted by residual: bond pdb=" C ILE C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 1.331 1.410 -0.079 1.20e-02 6.94e+03 4.29e+01 bond pdb=" C ILE D 68 " pdb=" N PRO D 69 " ideal model delta sigma weight residual 1.331 1.410 -0.078 1.20e-02 6.94e+03 4.28e+01 bond pdb=" N ARG C 186 " pdb=" CA ARG C 186 " ideal model delta sigma weight residual 1.458 1.483 -0.024 1.26e-02 6.30e+03 3.73e+00 bond pdb=" N ARG C 175 " pdb=" CA ARG C 175 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.48e-02 4.57e+03 3.69e+00 bond pdb=" N ARG D 175 " pdb=" CA ARG D 175 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.48e-02 4.57e+03 3.63e+00 ... (remaining 8797 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.78: 182 105.78 - 112.83: 4509 112.83 - 119.88: 3243 119.88 - 126.93: 3868 126.93 - 133.98: 116 Bond angle restraints: 11918 Sorted by residual: angle pdb=" C ASP A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C ASP B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C ALA A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ALA B 47 " pdb=" N ASP B 48 " pdb=" CA ASP B 48 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ALA B 170 " pdb=" N LEU B 171 " pdb=" CA LEU B 171 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 ... (remaining 11913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 4674 15.32 - 30.65: 394 30.65 - 45.97: 110 45.97 - 61.30: 11 61.30 - 76.62: 3 Dihedral angle restraints: 5192 sinusoidal: 2090 harmonic: 3102 Sorted by residual: dihedral pdb=" CD ARG C 175 " pdb=" NE ARG C 175 " pdb=" CZ ARG C 175 " pdb=" NH1 ARG C 175 " ideal model delta sinusoidal sigma weight residual 0.00 76.62 -76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CA ALA B 87 " pdb=" C ALA B 87 " pdb=" N SER B 88 " pdb=" CA SER B 88 " ideal model delta harmonic sigma weight residual 180.00 142.60 37.40 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CA ALA A 87 " pdb=" C ALA A 87 " pdb=" N SER A 88 " pdb=" CA SER A 88 " ideal model delta harmonic sigma weight residual 180.00 142.63 37.37 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 759 0.048 - 0.095: 413 0.095 - 0.143: 126 0.143 - 0.191: 42 0.191 - 0.238: 10 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE C 59 " pdb=" CA ILE C 59 " pdb=" CG1 ILE C 59 " pdb=" CG2 ILE C 59 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE D 59 " pdb=" CA ILE D 59 " pdb=" CG1 ILE D 59 " pdb=" CG2 ILE D 59 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1347 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 175 " -1.068 9.50e-02 1.11e+02 4.79e-01 1.38e+02 pdb=" NE ARG C 175 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 175 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 175 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 175 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 175 " 0.986 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG D 175 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG D 175 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 175 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 175 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 100 " -0.920 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG D 100 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG D 100 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 100 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 100 " -0.024 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2191 2.79 - 3.32: 8165 3.32 - 3.84: 13283 3.84 - 4.37: 15766 4.37 - 4.90: 25436 Nonbonded interactions: 64841 Sorted by model distance: nonbonded pdb=" OG1 THR D 138 " pdb=" O TYR D 140 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR C 138 " pdb=" O TYR C 140 " model vdw 2.261 2.440 nonbonded pdb=" OE1 GLU D 219 " pdb=" OH TYR D 231 " model vdw 2.267 2.440 nonbonded pdb=" OE1 GLU C 219 " pdb=" OH TYR C 231 " model vdw 2.267 2.440 nonbonded pdb=" OG SER A 21 " pdb=" OE1 GLU A 22 " model vdw 2.318 2.440 ... (remaining 64836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.370 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: 0.010 Extract box with map and model: 2.350 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 26.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.007 0.079 8802 Z= 0.442 Angle : 1.225 12.267 11918 Z= 0.636 Chirality : 0.066 0.238 1350 Planarity : 0.028 0.479 1468 Dihedral : 12.504 76.622 3204 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.33 % Favored : 85.48 % Rotamer: Outliers : 0.53 % Allowed : 8.19 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -5.84 (0.18), residues: 1054 helix: -3.92 (0.13), residues: 498 sheet: -3.55 (0.55), residues: 46 loop : -3.87 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 215 HIS 0.011 0.002 HIS C 124 PHE 0.038 0.003 PHE C 264 TYR 0.027 0.003 TYR B 14 ARG 0.007 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 392 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: -0.1097 (tpp) cc_final: -0.1875 (mpp) REVERT: A 38 TYR cc_start: 0.8712 (m-80) cc_final: 0.7987 (m-80) REVERT: A 84 ASP cc_start: 0.7513 (m-30) cc_final: 0.7119 (m-30) REVERT: A 132 ASP cc_start: 0.8022 (t0) cc_final: 0.7372 (t0) REVERT: A 186 MET cc_start: 0.9423 (mmt) cc_final: 0.9174 (mmp) REVERT: A 192 ARG cc_start: 0.8269 (ttm170) cc_final: 0.8009 (ttm170) REVERT: A 214 LEU cc_start: 0.9248 (mt) cc_final: 0.9023 (tt) REVERT: B 27 MET cc_start: -0.1029 (tpp) cc_final: -0.1761 (mpp) REVERT: B 38 TYR cc_start: 0.8483 (m-80) cc_final: 0.8007 (m-80) REVERT: B 104 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 107 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8699 (tt0) REVERT: B 132 ASP cc_start: 0.8004 (t0) cc_final: 0.7437 (t0) REVERT: B 214 LEU cc_start: 0.9195 (mt) cc_final: 0.8875 (tt) REVERT: B 251 GLN cc_start: 0.8215 (tp40) cc_final: 0.7753 (tp40) REVERT: B 264 PHE cc_start: 0.7159 (t80) cc_final: 0.6927 (t80) REVERT: C 14 ASN cc_start: 0.9211 (m-40) cc_final: 0.8949 (m-40) REVERT: C 70 PHE cc_start: 0.6162 (t80) cc_final: 0.5839 (t80) REVERT: C 86 GLN cc_start: 0.8696 (pp30) cc_final: 0.8485 (pp30) REVERT: C 112 ILE cc_start: 0.9700 (tp) cc_final: 0.9488 (mt) REVERT: C 126 MET cc_start: 0.6721 (tpp) cc_final: 0.5864 (tpp) REVERT: C 132 PHE cc_start: 0.8268 (m-10) cc_final: 0.7776 (m-10) REVERT: C 136 GLN cc_start: 0.8915 (mt0) cc_final: 0.8385 (mm110) REVERT: C 142 VAL cc_start: 0.8703 (m) cc_final: 0.8078 (m) REVERT: C 180 ILE cc_start: 0.9548 (mm) cc_final: 0.9333 (mt) REVERT: C 259 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8095 (tmtt) REVERT: C 266 ASP cc_start: 0.8334 (p0) cc_final: 0.7261 (p0) REVERT: D 6 THR cc_start: 0.9703 (p) cc_final: 0.9380 (p) REVERT: D 14 ASN cc_start: 0.9254 (m-40) cc_final: 0.9048 (m-40) REVERT: D 126 MET cc_start: 0.7038 (tpp) cc_final: 0.6180 (tpp) REVERT: D 132 PHE cc_start: 0.8227 (m-10) cc_final: 0.7721 (m-10) REVERT: D 136 GLN cc_start: 0.8629 (mt0) cc_final: 0.8344 (mm110) REVERT: D 142 VAL cc_start: 0.8917 (m) cc_final: 0.8431 (m) REVERT: D 180 ILE cc_start: 0.9592 (mm) cc_final: 0.9332 (mt) REVERT: D 266 ASP cc_start: 0.8246 (p0) cc_final: 0.7242 (p0) outliers start: 5 outliers final: 2 residues processed: 394 average time/residue: 0.2391 time to fit residues: 122.3132 Evaluate side-chains 209 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 186 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 81 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 251 GLN B 187 ASN C 32 ASN ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 200 HIS D 32 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 257 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8802 Z= 0.213 Angle : 0.875 10.326 11918 Z= 0.443 Chirality : 0.049 0.257 1350 Planarity : 0.005 0.038 1468 Dihedral : 7.457 30.129 1172 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.23 % Favored : 85.58 % Rotamer: Outliers : 3.19 % Allowed : 15.64 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.67 (0.21), residues: 1054 helix: -2.66 (0.18), residues: 524 sheet: -2.62 (0.69), residues: 44 loop : -3.65 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 52 HIS 0.009 0.001 HIS D 257 PHE 0.038 0.002 PHE D 70 TYR 0.036 0.002 TYR C 215 ARG 0.008 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: -0.0811 (tpp) cc_final: -0.1402 (mpp) REVERT: A 38 TYR cc_start: 0.8640 (m-80) cc_final: 0.7923 (m-80) REVERT: A 251 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7821 (tp-100) REVERT: B 11 THR cc_start: 0.8961 (m) cc_final: 0.8490 (t) REVERT: B 27 MET cc_start: -0.1233 (tpp) cc_final: -0.1817 (mpp) REVERT: B 38 TYR cc_start: 0.8699 (m-80) cc_final: 0.7966 (m-80) REVERT: B 251 GLN cc_start: 0.8542 (tp40) cc_final: 0.7804 (tp40) REVERT: C 38 LEU cc_start: 0.8113 (mm) cc_final: 0.7434 (mm) REVERT: C 105 MET cc_start: 0.8824 (mpt) cc_final: 0.8127 (mpp) REVERT: C 136 GLN cc_start: 0.8779 (mt0) cc_final: 0.8283 (mm110) REVERT: C 182 GLN cc_start: 0.9023 (tt0) cc_final: 0.8792 (tt0) REVERT: C 206 GLN cc_start: 0.8713 (tt0) cc_final: 0.8427 (tt0) REVERT: C 219 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8315 (mm-30) REVERT: C 259 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8232 (tmtt) REVERT: C 266 ASP cc_start: 0.8259 (p0) cc_final: 0.7309 (p0) REVERT: D 25 GLU cc_start: 0.8642 (mp0) cc_final: 0.8302 (mp0) REVERT: D 38 LEU cc_start: 0.8086 (mm) cc_final: 0.6584 (mm) REVERT: D 70 PHE cc_start: 0.6862 (t80) cc_final: 0.6384 (t80) REVERT: D 86 GLN cc_start: 0.8854 (pp30) cc_final: 0.8585 (pp30) REVERT: D 254 SER cc_start: 0.9622 (OUTLIER) cc_final: 0.9238 (t) REVERT: D 259 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8320 (tmtt) REVERT: D 266 ASP cc_start: 0.8239 (p0) cc_final: 0.7161 (p0) outliers start: 30 outliers final: 18 residues processed: 282 average time/residue: 0.1755 time to fit residues: 70.2568 Evaluate side-chains 232 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 78 optimal weight: 0.0270 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN C 30 ASN C 200 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8802 Z= 0.243 Angle : 0.833 8.764 11918 Z= 0.415 Chirality : 0.049 0.248 1350 Planarity : 0.004 0.031 1468 Dihedral : 6.945 31.917 1164 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.61 % Favored : 85.29 % Rotamer: Outliers : 5.53 % Allowed : 18.62 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.88 (0.23), residues: 1054 helix: -1.84 (0.20), residues: 516 sheet: -2.76 (0.68), residues: 46 loop : -3.41 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 81 HIS 0.005 0.001 HIS C 124 PHE 0.020 0.001 PHE D 70 TYR 0.025 0.002 TYR D 215 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 221 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: -0.0844 (tpp) cc_final: -0.1517 (mpp) REVERT: A 38 TYR cc_start: 0.8699 (m-80) cc_final: 0.7986 (m-80) REVERT: A 41 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7339 (mtp85) REVERT: A 251 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7817 (tp-100) REVERT: B 5 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8090 (m) REVERT: B 16 LEU cc_start: 0.8338 (tm) cc_final: 0.7911 (tm) REVERT: B 27 MET cc_start: -0.1139 (tpp) cc_final: -0.1821 (mpp) REVERT: B 190 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8797 (mttt) REVERT: B 218 TYR cc_start: 0.8716 (m-10) cc_final: 0.8503 (m-10) REVERT: B 251 GLN cc_start: 0.8576 (tp-100) cc_final: 0.7924 (tp-100) REVERT: C 30 ASN cc_start: 0.6352 (t0) cc_final: 0.5954 (t0) REVERT: C 206 GLN cc_start: 0.8719 (tt0) cc_final: 0.8424 (tt0) REVERT: C 215 TYR cc_start: 0.8868 (t80) cc_final: 0.8466 (t80) REVERT: C 219 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 225 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8360 (pp) REVERT: C 234 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7721 (p0) REVERT: C 259 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8324 (tmtt) REVERT: C 266 ASP cc_start: 0.8235 (p0) cc_final: 0.7184 (p0) REVERT: D 25 GLU cc_start: 0.8697 (mp0) cc_final: 0.8355 (mp0) REVERT: D 86 GLN cc_start: 0.8824 (pp30) cc_final: 0.8564 (pp30) REVERT: D 165 LEU cc_start: 0.9378 (mp) cc_final: 0.9099 (mp) REVERT: D 225 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8337 (pp) REVERT: D 259 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8300 (tmtt) REVERT: D 266 ASP cc_start: 0.8133 (p0) cc_final: 0.6997 (p0) outliers start: 52 outliers final: 28 residues processed: 260 average time/residue: 0.1670 time to fit residues: 62.6995 Evaluate side-chains 239 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 200 HIS D 47 GLN D 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8802 Z= 0.196 Angle : 0.805 9.771 11918 Z= 0.397 Chirality : 0.048 0.275 1350 Planarity : 0.004 0.032 1468 Dihedral : 6.614 28.215 1164 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Rotamer: Outliers : 4.47 % Allowed : 20.64 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.25), residues: 1054 helix: -1.24 (0.22), residues: 512 sheet: -2.69 (0.69), residues: 46 loop : -3.16 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 52 HIS 0.005 0.001 HIS C 257 PHE 0.013 0.001 PHE D 70 TYR 0.023 0.002 TYR D 215 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 1.215 Fit side-chains REVERT: A 27 MET cc_start: -0.0747 (tpp) cc_final: -0.1349 (mpp) REVERT: A 38 TYR cc_start: 0.8706 (m-80) cc_final: 0.7991 (m-80) REVERT: A 41 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7411 (mtp85) REVERT: A 152 LEU cc_start: 0.9766 (tp) cc_final: 0.9466 (tt) REVERT: A 156 ILE cc_start: 0.9363 (mp) cc_final: 0.9093 (mp) REVERT: A 190 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8937 (mttt) REVERT: A 251 GLN cc_start: 0.8450 (tp-100) cc_final: 0.7797 (tp-100) REVERT: B 27 MET cc_start: -0.1093 (tpp) cc_final: -0.1740 (mpp) REVERT: B 190 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mttt) REVERT: B 251 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7908 (tp-100) REVERT: B 264 PHE cc_start: 0.7255 (t80) cc_final: 0.6917 (m-80) REVERT: C 9 MET cc_start: 0.8667 (mmm) cc_final: 0.8459 (mmt) REVERT: C 30 ASN cc_start: 0.6272 (t0) cc_final: 0.5841 (t0) REVERT: C 189 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8980 (tp) REVERT: C 215 TYR cc_start: 0.8925 (t80) cc_final: 0.8367 (t80) REVERT: C 219 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 225 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (pp) REVERT: C 259 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8299 (tmtt) REVERT: C 266 ASP cc_start: 0.8184 (p0) cc_final: 0.7215 (p0) REVERT: D 25 GLU cc_start: 0.8659 (mp0) cc_final: 0.8379 (mp0) REVERT: D 86 GLN cc_start: 0.8868 (pp30) cc_final: 0.8573 (pp30) REVERT: D 136 GLN cc_start: 0.8597 (mt0) cc_final: 0.8261 (mm110) REVERT: D 165 LEU cc_start: 0.9388 (mp) cc_final: 0.9186 (mm) REVERT: D 206 GLN cc_start: 0.8654 (tt0) cc_final: 0.8410 (tm-30) REVERT: D 234 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7815 (p0) REVERT: D 259 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8253 (tmtt) REVERT: D 266 ASP cc_start: 0.8146 (p0) cc_final: 0.7164 (p0) outliers start: 42 outliers final: 22 residues processed: 268 average time/residue: 0.1752 time to fit residues: 67.6218 Evaluate side-chains 243 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN B 205 GLN B 260 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 47 GLN D 124 HIS D 200 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8802 Z= 0.394 Angle : 0.883 11.666 11918 Z= 0.447 Chirality : 0.051 0.289 1350 Planarity : 0.005 0.033 1468 Dihedral : 6.638 27.005 1164 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.98 % Favored : 82.83 % Rotamer: Outliers : 5.32 % Allowed : 20.43 % Favored : 74.26 % 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: -3.27 (0.25), residues: 1054 helix: -1.31 (0.21), residues: 564 sheet: -2.41 (0.74), residues: 46 loop : -3.30 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 52 HIS 0.008 0.001 HIS D 124 PHE 0.012 0.002 PHE D 70 TYR 0.027 0.003 TYR A 14 ARG 0.008 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 1.018 Fit side-chains REVERT: A 27 MET cc_start: -0.1188 (tpp) cc_final: -0.2083 (mpp) REVERT: A 38 TYR cc_start: 0.8909 (m-80) cc_final: 0.7929 (m-80) REVERT: A 190 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (mttt) REVERT: A 251 GLN cc_start: 0.8547 (tp-100) cc_final: 0.7881 (tp-100) REVERT: A 257 MET cc_start: 0.8670 (mmt) cc_final: 0.8325 (mtt) REVERT: A 264 PHE cc_start: 0.7268 (t80) cc_final: 0.6730 (m-80) REVERT: B 27 MET cc_start: -0.1457 (tpp) cc_final: -0.2330 (mpp) REVERT: B 251 GLN cc_start: 0.8617 (tp-100) cc_final: 0.7988 (tp-100) REVERT: B 264 PHE cc_start: 0.7227 (t80) cc_final: 0.6728 (m-80) REVERT: C 30 ASN cc_start: 0.6588 (t0) cc_final: 0.6374 (t0) REVERT: C 189 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9108 (tp) REVERT: C 206 GLN cc_start: 0.8654 (tt0) cc_final: 0.8437 (mt0) REVERT: C 215 TYR cc_start: 0.9096 (t80) cc_final: 0.8464 (t80) REVERT: C 219 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 225 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8457 (pp) REVERT: C 234 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7928 (p0) REVERT: C 259 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8435 (tmtt) REVERT: C 266 ASP cc_start: 0.8513 (p0) cc_final: 0.7438 (p0) REVERT: D 14 ASN cc_start: 0.9200 (m-40) cc_final: 0.8878 (m-40) REVERT: D 86 GLN cc_start: 0.8891 (pp30) cc_final: 0.8583 (pp30) REVERT: D 165 LEU cc_start: 0.9449 (mp) cc_final: 0.9236 (mm) REVERT: D 225 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8328 (pp) REVERT: D 234 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7897 (p0) REVERT: D 259 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8397 (tmtt) REVERT: D 266 ASP cc_start: 0.8365 (p0) cc_final: 0.7293 (p0) outliers start: 50 outliers final: 34 residues processed: 251 average time/residue: 0.1700 time to fit residues: 61.0063 Evaluate side-chains 236 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN B 205 GLN C 30 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 200 HIS D 200 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8802 Z= 0.224 Angle : 0.819 10.620 11918 Z= 0.404 Chirality : 0.048 0.203 1350 Planarity : 0.004 0.052 1468 Dihedral : 6.480 26.913 1164 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 4.47 % Allowed : 22.45 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 1054 helix: -1.00 (0.22), residues: 554 sheet: -2.15 (0.75), residues: 46 loop : -3.22 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 52 HIS 0.005 0.001 HIS C 257 PHE 0.045 0.001 PHE C 70 TYR 0.017 0.002 TYR D 151 ARG 0.003 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: -0.1209 (tpp) cc_final: -0.2092 (mpp) REVERT: A 38 TYR cc_start: 0.8866 (m-80) cc_final: 0.8650 (m-80) REVERT: A 41 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7410 (mtp85) REVERT: A 152 LEU cc_start: 0.9751 (tp) cc_final: 0.9462 (tt) REVERT: A 156 ILE cc_start: 0.9444 (mt) cc_final: 0.9191 (mp) REVERT: A 190 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8909 (mttt) REVERT: A 251 GLN cc_start: 0.8462 (tp-100) cc_final: 0.7835 (tp-100) REVERT: A 257 MET cc_start: 0.8640 (mmt) cc_final: 0.8248 (mtm) REVERT: B 27 MET cc_start: -0.1556 (tpp) cc_final: -0.2485 (mpp) REVERT: B 190 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8950 (mttt) REVERT: B 251 GLN cc_start: 0.8598 (tp-100) cc_final: 0.7955 (tp-100) REVERT: B 264 PHE cc_start: 0.7219 (t80) cc_final: 0.6919 (m-80) REVERT: C 30 ASN cc_start: 0.6592 (t0) cc_final: 0.6361 (t0) REVERT: C 189 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9014 (tp) REVERT: C 206 GLN cc_start: 0.8603 (tt0) cc_final: 0.8075 (mt0) REVERT: C 259 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8423 (tmtt) REVERT: C 266 ASP cc_start: 0.8337 (p0) cc_final: 0.7331 (p0) REVERT: D 25 GLU cc_start: 0.8471 (mp0) cc_final: 0.8180 (mp0) REVERT: D 86 GLN cc_start: 0.8903 (pp30) cc_final: 0.8617 (pp30) REVERT: D 165 LEU cc_start: 0.9491 (mp) cc_final: 0.9259 (mm) REVERT: D 225 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8212 (pp) REVERT: D 234 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7911 (p0) REVERT: D 235 HIS cc_start: 0.8609 (m90) cc_final: 0.8351 (m90) REVERT: D 259 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8479 (tmtt) REVERT: D 266 ASP cc_start: 0.8347 (p0) cc_final: 0.7387 (p0) outliers start: 42 outliers final: 30 residues processed: 253 average time/residue: 0.1653 time to fit residues: 59.8797 Evaluate side-chains 240 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8802 Z= 0.204 Angle : 0.813 11.454 11918 Z= 0.397 Chirality : 0.048 0.291 1350 Planarity : 0.004 0.028 1468 Dihedral : 6.317 26.498 1164 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.84 % Favored : 84.16 % Rotamer: Outliers : 5.00 % Allowed : 23.62 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.26), residues: 1054 helix: -0.93 (0.22), residues: 558 sheet: -1.75 (0.78), residues: 46 loop : -3.25 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 52 HIS 0.005 0.001 HIS D 124 PHE 0.018 0.001 PHE C 242 TYR 0.016 0.002 TYR D 151 ARG 0.003 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 1.043 Fit side-chains REVERT: A 27 MET cc_start: -0.1290 (tpp) cc_final: -0.2150 (mpp) REVERT: A 38 TYR cc_start: 0.8892 (m-80) cc_final: 0.7990 (m-80) REVERT: A 41 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7302 (mtp85) REVERT: A 152 LEU cc_start: 0.9738 (tp) cc_final: 0.9428 (tt) REVERT: A 156 ILE cc_start: 0.9414 (mt) cc_final: 0.9149 (mp) REVERT: A 190 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8910 (mttt) REVERT: A 251 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7807 (tp-100) REVERT: A 257 MET cc_start: 0.8588 (mmt) cc_final: 0.8180 (mtm) REVERT: B 27 MET cc_start: -0.1417 (tpp) cc_final: -0.2402 (mpp) REVERT: B 190 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8952 (mttt) REVERT: B 251 GLN cc_start: 0.8544 (tp-100) cc_final: 0.7914 (tp-100) REVERT: B 257 MET cc_start: 0.8509 (mmt) cc_final: 0.8260 (mtm) REVERT: C 27 LYS cc_start: 0.8702 (tttp) cc_final: 0.8453 (tttm) REVERT: C 189 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8982 (tp) REVERT: C 206 GLN cc_start: 0.8576 (tt0) cc_final: 0.8074 (mt0) REVERT: C 234 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7858 (p0) REVERT: C 259 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8762 (mmmt) REVERT: C 266 ASP cc_start: 0.8377 (p0) cc_final: 0.7294 (p0) REVERT: D 25 GLU cc_start: 0.8410 (mp0) cc_final: 0.8121 (mp0) REVERT: D 86 GLN cc_start: 0.8890 (pp30) cc_final: 0.8619 (pp30) REVERT: D 165 LEU cc_start: 0.9484 (mp) cc_final: 0.9231 (mm) REVERT: D 225 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (pp) REVERT: D 234 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7962 (p0) REVERT: D 259 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8478 (tmtt) REVERT: D 266 ASP cc_start: 0.8332 (p0) cc_final: 0.7283 (p0) outliers start: 47 outliers final: 35 residues processed: 260 average time/residue: 0.1658 time to fit residues: 61.7947 Evaluate side-chains 248 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8802 Z= 0.192 Angle : 0.818 11.812 11918 Z= 0.399 Chirality : 0.048 0.224 1350 Planarity : 0.004 0.027 1468 Dihedral : 6.213 29.478 1164 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % Rotamer: Outliers : 5.21 % Allowed : 24.04 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.26), residues: 1054 helix: -0.81 (0.22), residues: 552 sheet: -1.41 (0.78), residues: 46 loop : -3.14 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 81 HIS 0.005 0.001 HIS C 124 PHE 0.024 0.001 PHE B 264 TYR 0.016 0.002 TYR D 151 ARG 0.004 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 1.125 Fit side-chains REVERT: A 27 MET cc_start: -0.1290 (tpp) cc_final: -0.2165 (mpp) REVERT: A 38 TYR cc_start: 0.8956 (m-80) cc_final: 0.7927 (m-80) REVERT: A 41 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7267 (mtp85) REVERT: A 152 LEU cc_start: 0.9728 (tp) cc_final: 0.9406 (tt) REVERT: A 156 ILE cc_start: 0.9385 (mt) cc_final: 0.9084 (mp) REVERT: A 251 GLN cc_start: 0.8396 (tp-100) cc_final: 0.7762 (tp-100) REVERT: A 257 MET cc_start: 0.8573 (mmt) cc_final: 0.8162 (mtm) REVERT: B 27 MET cc_start: -0.1298 (tpp) cc_final: -0.2300 (mpp) REVERT: B 190 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8938 (mttt) REVERT: B 251 GLN cc_start: 0.8552 (tp-100) cc_final: 0.7932 (tp-100) REVERT: B 257 MET cc_start: 0.8453 (mmt) cc_final: 0.8243 (mtm) REVERT: C 189 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8973 (tp) REVERT: C 206 GLN cc_start: 0.8568 (tt0) cc_final: 0.8118 (mt0) REVERT: C 225 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8217 (pp) REVERT: C 234 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (p0) REVERT: C 259 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8699 (mmmt) REVERT: C 266 ASP cc_start: 0.8414 (p0) cc_final: 0.7412 (p0) REVERT: D 25 GLU cc_start: 0.8497 (mp0) cc_final: 0.8147 (mp0) REVERT: D 86 GLN cc_start: 0.8885 (pp30) cc_final: 0.8391 (pp30) REVERT: D 165 LEU cc_start: 0.9483 (mp) cc_final: 0.9243 (mm) REVERT: D 204 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8353 (mm) REVERT: D 225 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8204 (pp) REVERT: D 234 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7888 (p0) REVERT: D 259 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8460 (tmtt) REVERT: D 266 ASP cc_start: 0.8276 (p0) cc_final: 0.7202 (p0) outliers start: 49 outliers final: 33 residues processed: 263 average time/residue: 0.1631 time to fit residues: 62.1847 Evaluate side-chains 254 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8802 Z= 0.176 Angle : 0.823 11.301 11918 Z= 0.394 Chirality : 0.047 0.217 1350 Planarity : 0.004 0.028 1468 Dihedral : 6.062 27.791 1164 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.99 % Favored : 85.01 % Rotamer: Outliers : 4.15 % Allowed : 25.11 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 1054 helix: -0.63 (0.23), residues: 538 sheet: -0.65 (0.87), residues: 46 loop : -3.04 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 81 HIS 0.005 0.001 HIS C 124 PHE 0.020 0.001 PHE C 242 TYR 0.034 0.002 TYR C 215 ARG 0.003 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 1.097 Fit side-chains REVERT: A 27 MET cc_start: -0.1469 (tpp) cc_final: -0.2388 (mpp) REVERT: A 38 TYR cc_start: 0.8947 (m-80) cc_final: 0.7855 (m-80) REVERT: A 152 LEU cc_start: 0.9677 (tp) cc_final: 0.9300 (tt) REVERT: A 156 ILE cc_start: 0.9339 (mt) cc_final: 0.9114 (mp) REVERT: A 251 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7781 (tp-100) REVERT: A 257 MET cc_start: 0.8588 (mmt) cc_final: 0.8186 (mtm) REVERT: B 27 MET cc_start: -0.1295 (tpp) cc_final: -0.2296 (mpp) REVERT: B 104 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 190 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8929 (mttt) REVERT: B 251 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7945 (tp-100) REVERT: B 257 MET cc_start: 0.8445 (mmt) cc_final: 0.8222 (mtm) REVERT: C 52 TRP cc_start: 0.9324 (t60) cc_final: 0.9057 (t60) REVERT: C 166 ILE cc_start: 0.8888 (mm) cc_final: 0.8631 (mm) REVERT: C 167 THR cc_start: 0.8891 (p) cc_final: 0.8685 (p) REVERT: C 204 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8495 (mm) REVERT: C 206 GLN cc_start: 0.8510 (tt0) cc_final: 0.8247 (mt0) REVERT: C 219 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 225 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 234 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7873 (p0) REVERT: C 266 ASP cc_start: 0.8217 (p0) cc_final: 0.7196 (p0) REVERT: D 25 GLU cc_start: 0.8540 (mp0) cc_final: 0.8255 (mp0) REVERT: D 86 GLN cc_start: 0.8599 (pp30) cc_final: 0.8365 (pp30) REVERT: D 165 LEU cc_start: 0.9467 (mp) cc_final: 0.9209 (mm) REVERT: D 204 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8287 (mm) REVERT: D 206 GLN cc_start: 0.8662 (tt0) cc_final: 0.8271 (tm-30) REVERT: D 215 TYR cc_start: 0.8995 (t80) cc_final: 0.8698 (t80) REVERT: D 219 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8416 (mm-30) REVERT: D 225 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8002 (pp) REVERT: D 234 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7829 (p0) REVERT: D 259 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8440 (tmtt) REVERT: D 266 ASP cc_start: 0.8246 (p0) cc_final: 0.7237 (p0) outliers start: 39 outliers final: 24 residues processed: 258 average time/residue: 0.1692 time to fit residues: 63.1771 Evaluate side-chains 250 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 32 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8802 Z= 0.201 Angle : 0.843 15.183 11918 Z= 0.401 Chirality : 0.047 0.195 1350 Planarity : 0.004 0.030 1468 Dihedral : 5.960 27.421 1164 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % Rotamer: Outliers : 3.72 % Allowed : 26.60 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.26), residues: 1054 helix: -0.55 (0.23), residues: 540 sheet: -0.58 (0.87), residues: 46 loop : -3.00 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 81 HIS 0.006 0.001 HIS D 124 PHE 0.020 0.001 PHE D 242 TYR 0.024 0.002 TYR C 215 ARG 0.003 0.000 ARG A 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 1.143 Fit side-chains REVERT: A 27 MET cc_start: -0.1469 (tpp) cc_final: -0.2394 (mpp) REVERT: A 38 TYR cc_start: 0.8968 (m-80) cc_final: 0.7868 (m-80) REVERT: A 152 LEU cc_start: 0.9683 (tp) cc_final: 0.9309 (tt) REVERT: A 156 ILE cc_start: 0.9373 (mt) cc_final: 0.9146 (mp) REVERT: A 251 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7817 (tp-100) REVERT: A 257 MET cc_start: 0.8694 (mmt) cc_final: 0.8233 (mtm) REVERT: B 27 MET cc_start: -0.0943 (tpp) cc_final: -0.2073 (mpp) REVERT: B 104 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 190 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8925 (mttt) REVERT: B 251 GLN cc_start: 0.8575 (tp-100) cc_final: 0.7970 (tp-100) REVERT: C 52 TRP cc_start: 0.9312 (t60) cc_final: 0.9041 (t60) REVERT: C 53 PHE cc_start: 0.7962 (t80) cc_final: 0.7537 (t80) REVERT: C 166 ILE cc_start: 0.8878 (mm) cc_final: 0.8624 (mm) REVERT: C 167 THR cc_start: 0.8892 (p) cc_final: 0.8686 (p) REVERT: C 204 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8501 (mm) REVERT: C 206 GLN cc_start: 0.8466 (tt0) cc_final: 0.8063 (mt0) REVERT: C 219 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 225 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8276 (pp) REVERT: C 234 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7872 (p0) REVERT: C 266 ASP cc_start: 0.8245 (p0) cc_final: 0.7214 (p0) REVERT: D 25 GLU cc_start: 0.8528 (mp0) cc_final: 0.8264 (mp0) REVERT: D 86 GLN cc_start: 0.8562 (pp30) cc_final: 0.8330 (pp30) REVERT: D 165 LEU cc_start: 0.9483 (mp) cc_final: 0.9234 (mm) REVERT: D 204 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (mm) REVERT: D 206 GLN cc_start: 0.8684 (tt0) cc_final: 0.8349 (tm-30) REVERT: D 215 TYR cc_start: 0.9033 (t80) cc_final: 0.8592 (t80) REVERT: D 219 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 225 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8052 (pp) REVERT: D 234 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7810 (p0) REVERT: D 259 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8452 (tmtt) REVERT: D 266 ASP cc_start: 0.8291 (p0) cc_final: 0.7278 (p0) outliers start: 35 outliers final: 26 residues processed: 241 average time/residue: 0.1609 time to fit residues: 56.6922 Evaluate side-chains 241 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 84 optimal weight: 0.0030 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS D 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083483 restraints weight = 23100.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085709 restraints weight = 13984.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.087229 restraints weight = 9934.186| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8802 Z= 0.188 Angle : 0.837 14.747 11918 Z= 0.400 Chirality : 0.047 0.194 1350 Planarity : 0.004 0.030 1468 Dihedral : 5.878 27.378 1164 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Rotamer: Outliers : 3.72 % Allowed : 26.81 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.27), residues: 1054 helix: -0.46 (0.23), residues: 540 sheet: -0.65 (0.86), residues: 46 loop : -2.97 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 81 HIS 0.006 0.001 HIS C 124 PHE 0.019 0.001 PHE C 242 TYR 0.021 0.002 TYR C 215 ARG 0.004 0.000 ARG B 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.79 seconds wall clock time: 36 minutes 50.57 seconds (2210.57 seconds total)