Starting phenix.real_space_refine on Sat Mar 16 00:14:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7p_32346/03_2024/7w7p_32346.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 89 5.16 5 C 8337 2.51 5 N 2255 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E ASP 229": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "B" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2242 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "D" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2248 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "F" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2248 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Time building chain proxies: 7.37, per 1000 atoms: 0.56 Number of scatterers: 13176 At special positions: 0 Unit cell: (147, 140, 85, 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 89 16.00 O 2495 8.00 N 2255 7.00 C 8337 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: 5.37 Conformation dependent library (CDL) restraints added in 2.4 seconds 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 33.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 23 removed outlier: 3.587A pdb=" N VAL A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.591A pdb=" N GLY A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.726A pdb=" N VAL A 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.669A pdb=" N GLN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 73 through 79 removed outlier: 4.026A pdb=" N ILE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 89 through 121 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.634A pdb=" N GLN C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.597A pdb=" N GLY C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 86 Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.580A pdb=" N VAL C 122 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.615A pdb=" N THR C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.518A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.167A pdb=" N GLN D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 73 through 79 removed outlier: 4.155A pdb=" N ILE D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 89 through 121 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 23 through 33 removed outlier: 4.026A pdb=" N GLN E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.524A pdb=" N GLY E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 86 Proline residue: E 69 - end of helix Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.609A pdb=" N VAL E 122 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 removed outlier: 3.854A pdb=" N THR E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.532A pdb=" N TYR F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 48 removed outlier: 3.619A pdb=" N LYS F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 89 through 121 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.315A pdb=" N TYR A 40 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.457A pdb=" N VAL A 44 " --> pdb=" O SER A 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 135 removed outlier: 6.847A pdb=" N LYS A 205 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR A 135 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 203 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N CYS A 221 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU A 263 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 223 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLU A 227 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 269 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 243 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 270 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR A 241 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL A 272 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP A 239 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.513A pdb=" N ILE B 62 " --> pdb=" O HIS B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.621A pdb=" N LEU B 179 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 225 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.621A pdb=" N LEU B 179 " --> pdb=" O VAL B 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 173 through 182 current: chain 'B' and resid 296 through 305 removed outlier: 4.186A pdb=" N LEU B 296 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 302 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR B 273 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 304 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 271 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 162 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 233 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 169 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER B 231 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 5.908A pdb=" N TYR C 40 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 45 removed outlier: 6.354A pdb=" N VAL C 44 " --> pdb=" O SER C 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 135 removed outlier: 6.932A pdb=" N LYS C 205 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR C 135 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU C 203 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 12.495A pdb=" N CYS C 221 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU C 263 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 223 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 262 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 249 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR C 243 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 270 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 241 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL C 272 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 239 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 240 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.739A pdb=" N ALA C 158 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 61 through 65 removed outlier: 5.510A pdb=" N ILE D 62 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 64 " --> pdb=" O TYR D 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 189 through 193 removed outlier: 3.605A pdb=" N LEU D 179 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA D 225 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 189 through 193 removed outlier: 3.605A pdb=" N LEU D 179 " --> pdb=" O VAL D 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 173 through 182 current: chain 'D' and resid 297 through 305 removed outlier: 3.583A pdb=" N VAL D 275 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 302 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 273 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 304 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR D 271 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 270 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 164 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 233 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 169 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER D 231 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 40 through 41 removed outlier: 5.921A pdb=" N TYR E 40 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 45 removed outlier: 6.342A pdb=" N VAL E 44 " --> pdb=" O SER E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 135 removed outlier: 6.804A pdb=" N LYS E 205 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR E 135 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU E 203 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N CYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N LEU E 265 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL E 223 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA E 267 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL E 225 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR E 269 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N GLU E 227 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N LYS E 271 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR E 243 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL E 270 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 241 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL E 272 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP E 239 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 244 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 126 " --> pdb=" O GLY E 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 144 removed outlier: 3.689A pdb=" N LEU E 141 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER E 197 " --> pdb=" O PHE E 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.781A pdb=" N ASP E 161 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 61 through 65 removed outlier: 5.510A pdb=" N ILE F 62 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR F 140 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 64 " --> pdb=" O TYR F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 189 through 193 removed outlier: 3.971A pdb=" N VAL F 192 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 179 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA F 225 " --> pdb=" O THR F 177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 189 through 193 removed outlier: 3.971A pdb=" N VAL F 192 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 179 " --> pdb=" O VAL F 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 173 through 182 current: chain 'F' and resid 297 through 306 removed outlier: 5.350A pdb=" N ILE F 299 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS F 277 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 301 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL F 275 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER F 305 " --> pdb=" O THR F 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 160 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS F 233 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 169 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER F 231 " --> pdb=" O VAL F 169 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1353 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: 3.27 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4370 1.34 - 1.46: 2643 1.46 - 1.58: 6299 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 13428 Sorted by residual: bond pdb=" C THR E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.37e+00 bond pdb=" C THR C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.333 1.352 -0.018 1.01e-02 9.80e+03 3.25e+00 bond pdb=" C MET A 94 " pdb=" N LYS A 95 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.32e-02 5.74e+03 2.23e+00 bond pdb=" CB PRO A 96 " pdb=" CG PRO A 96 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" N LEU D 194 " pdb=" CA LEU D 194 " ideal model delta sigma weight residual 1.462 1.448 0.014 1.05e-02 9.07e+03 1.83e+00 ... (remaining 13423 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.16: 440 107.16 - 113.88: 7663 113.88 - 120.61: 5326 120.61 - 127.34: 4642 127.34 - 134.06: 128 Bond angle restraints: 18199 Sorted by residual: angle pdb=" C HIS A 39 " pdb=" N TYR A 40 " pdb=" CA TYR A 40 " ideal model delta sigma weight residual 122.28 113.61 8.67 1.77e+00 3.19e-01 2.40e+01 angle pdb=" C CYS E 152 " pdb=" N LYS E 153 " pdb=" CA LYS E 153 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 106.21 110.54 -4.33 1.07e+00 8.73e-01 1.64e+01 angle pdb=" CA PRO A 96 " pdb=" N PRO A 96 " pdb=" CD PRO A 96 " ideal model delta sigma weight residual 112.00 106.69 5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" N CYS C 149 " pdb=" CA CYS C 149 " pdb=" C CYS C 149 " ideal model delta sigma weight residual 108.07 112.37 -4.30 1.38e+00 5.25e-01 9.70e+00 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7459 17.96 - 35.92: 618 35.92 - 53.89: 137 53.89 - 71.85: 31 71.85 - 89.81: 13 Dihedral angle restraints: 8258 sinusoidal: 3368 harmonic: 4890 Sorted by residual: dihedral pdb=" CA ARG E 199 " pdb=" C ARG E 199 " pdb=" N ASP E 200 " pdb=" CA ASP E 200 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG F 73 " pdb=" C ARG F 73 " pdb=" N GLU F 74 " pdb=" CA GLU F 74 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PRO E 252 " pdb=" C PRO E 252 " pdb=" N PHE E 253 " pdb=" CA PHE E 253 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 8255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1680 0.053 - 0.105: 356 0.105 - 0.158: 43 0.158 - 0.210: 5 0.210 - 0.263: 3 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CB ILE E 107 " pdb=" CA ILE E 107 " pdb=" CG1 ILE E 107 " pdb=" CG2 ILE E 107 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE B 299 " pdb=" CA ILE B 299 " pdb=" CG1 ILE B 299 " pdb=" CG2 ILE B 299 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU F 297 " pdb=" CB LEU F 297 " pdb=" CD1 LEU F 297 " pdb=" CD2 LEU F 297 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2084 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 95 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO A 96 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 173 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO B 174 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 173 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO F 174 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.048 5.00e-02 4.00e+02 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 604 2.73 - 3.27: 14133 3.27 - 3.81: 21996 3.81 - 4.36: 25681 4.36 - 4.90: 43502 Nonbonded interactions: 105916 Sorted by model distance: nonbonded pdb=" OH TYR A 18 " pdb=" OG1 THR A 48 " model vdw 2.183 2.440 nonbonded pdb=" O VAL D 182 " pdb=" OG1 THR D 216 " model vdw 2.187 2.440 nonbonded pdb=" OG1 THR B 281 " pdb=" OE1 GLU B 282 " model vdw 2.207 2.440 nonbonded pdb=" O VAL B 182 " pdb=" OG1 THR B 216 " model vdw 2.207 2.440 nonbonded pdb=" O PRO E 90 " pdb=" NH1 ARG E 93 " model vdw 2.207 2.520 ... (remaining 105911 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 15 through 282 or resid 294 through 308)) selection = (chain 'F' and (resid 15 through 282 or resid 294 through 308)) } 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: 0.780 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: 0.020 Extract box with map and model: 4.040 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 35.910 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13428 Z= 0.213 Angle : 0.680 8.673 18199 Z= 0.365 Chirality : 0.044 0.263 2087 Planarity : 0.006 0.132 2354 Dihedral : 14.560 89.810 5086 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1649 helix: 1.29 (0.23), residues: 467 sheet: -0.61 (0.29), residues: 297 loop : -0.36 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 250 HIS 0.004 0.001 HIS C 39 PHE 0.025 0.001 PHE A 143 TYR 0.019 0.002 TYR A 18 ARG 0.009 0.001 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.5396 (m-10) cc_final: 0.4840 (m-10) REVERT: B 255 GLU cc_start: 0.7342 (tt0) cc_final: 0.7106 (tt0) REVERT: B 277 LYS cc_start: 0.6543 (mttt) cc_final: 0.5845 (mttt) REVERT: D 235 GLN cc_start: 0.7670 (pp30) cc_final: 0.7330 (pp30) REVERT: E 56 ILE cc_start: 0.7785 (pt) cc_final: 0.7452 (pt) REVERT: E 141 LEU cc_start: 0.6345 (tp) cc_final: 0.6102 (tp) REVERT: E 228 ASP cc_start: 0.6550 (m-30) cc_final: 0.6327 (m-30) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.2658 time to fit residues: 197.0562 Evaluate side-chains 380 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS A 176 ASN B 38 GLN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN D 35 GLN D 46 GLN D 81 ASN D 147 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13428 Z= 0.221 Angle : 0.656 7.759 18199 Z= 0.334 Chirality : 0.045 0.180 2087 Planarity : 0.005 0.083 2354 Dihedral : 4.783 59.291 1820 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.88 % Allowed : 15.47 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1649 helix: 1.42 (0.24), residues: 480 sheet: -0.62 (0.27), residues: 351 loop : -0.29 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 250 HIS 0.011 0.001 HIS A 22 PHE 0.017 0.002 PHE C 63 TYR 0.014 0.002 TYR C 201 ARG 0.008 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 398 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6449 (mt) REVERT: A 166 TYR cc_start: 0.5534 (m-10) cc_final: 0.4894 (m-10) REVERT: A 239 ASP cc_start: 0.7444 (p0) cc_final: 0.7011 (p0) REVERT: B 149 LYS cc_start: 0.7325 (mmtt) cc_final: 0.7105 (mmtt) REVERT: B 238 MET cc_start: 0.6535 (tpp) cc_final: 0.6109 (tpp) REVERT: C 61 ASN cc_start: 0.7544 (m110) cc_final: 0.7326 (p0) outliers start: 43 outliers final: 30 residues processed: 416 average time/residue: 0.2563 time to fit residues: 150.1156 Evaluate side-chains 393 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 362 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 148 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.9774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 39 HIS A 255 GLN B 147 GLN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS F 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13428 Z= 0.210 Angle : 0.623 7.799 18199 Z= 0.317 Chirality : 0.044 0.245 2087 Planarity : 0.005 0.070 2354 Dihedral : 4.711 64.562 1820 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.82 % Allowed : 19.09 % Favored : 77.09 % 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: 0.13 (0.21), residues: 1649 helix: 1.37 (0.24), residues: 472 sheet: -0.43 (0.28), residues: 347 loop : -0.35 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 250 HIS 0.011 0.001 HIS E 39 PHE 0.030 0.002 PHE D 40 TYR 0.029 0.002 TYR E 59 ARG 0.005 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 397 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6967 (pp30) REVERT: A 31 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6431 (mt) REVERT: A 166 TYR cc_start: 0.5448 (m-10) cc_final: 0.4820 (m-10) REVERT: A 239 ASP cc_start: 0.7462 (p0) cc_final: 0.7018 (p0) REVERT: B 238 MET cc_start: 0.6614 (tpp) cc_final: 0.5882 (tpp) REVERT: D 94 LEU cc_start: 0.8022 (mt) cc_final: 0.7633 (mt) REVERT: E 75 LEU cc_start: 0.6796 (mt) cc_final: 0.6564 (mt) REVERT: F 297 LEU cc_start: 0.6328 (mm) cc_final: 0.6118 (mm) outliers start: 57 outliers final: 41 residues processed: 417 average time/residue: 0.2701 time to fit residues: 159.6758 Evaluate side-chains 398 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 355 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.0050 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 0.0570 chunk 78 optimal weight: 0.0060 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 21 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13428 Z= 0.173 Angle : 0.615 7.904 18199 Z= 0.309 Chirality : 0.043 0.163 2087 Planarity : 0.004 0.061 2354 Dihedral : 4.510 64.227 1820 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.55 % Allowed : 21.23 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1649 helix: 1.25 (0.24), residues: 473 sheet: -0.42 (0.28), residues: 352 loop : -0.34 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 19 HIS 0.007 0.001 HIS E 39 PHE 0.039 0.002 PHE D 40 TYR 0.020 0.001 TYR E 59 ARG 0.010 0.001 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 392 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.5361 (m-10) cc_final: 0.4736 (m-10) REVERT: B 40 PHE cc_start: 0.5841 (m-80) cc_final: 0.5540 (m-80) REVERT: B 238 MET cc_start: 0.6518 (tpp) cc_final: 0.5781 (tpp) REVERT: D 94 LEU cc_start: 0.7903 (mt) cc_final: 0.7601 (mt) REVERT: E 50 PHE cc_start: 0.6102 (m-80) cc_final: 0.5838 (m-80) REVERT: E 253 PHE cc_start: 0.3917 (p90) cc_final: 0.3638 (p90) REVERT: F 95 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6720 (tm-30) REVERT: F 238 MET cc_start: 0.6890 (tpp) cc_final: 0.6610 (tpt) outliers start: 53 outliers final: 38 residues processed: 414 average time/residue: 0.2624 time to fit residues: 151.8974 Evaluate side-chains 392 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 354 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain E residue 273 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13428 Z= 0.193 Angle : 0.620 8.347 18199 Z= 0.313 Chirality : 0.043 0.189 2087 Planarity : 0.005 0.069 2354 Dihedral : 4.479 63.898 1820 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.42 % Allowed : 21.63 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1649 helix: 1.27 (0.24), residues: 480 sheet: -0.53 (0.27), residues: 372 loop : -0.26 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 19 HIS 0.005 0.001 HIS E 22 PHE 0.030 0.002 PHE D 40 TYR 0.020 0.001 TYR A 40 ARG 0.012 0.001 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 371 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6417 (mt) REVERT: A 166 TYR cc_start: 0.5315 (m-10) cc_final: 0.4659 (m-10) REVERT: A 239 ASP cc_start: 0.7318 (p0) cc_final: 0.7027 (p0) REVERT: B 40 PHE cc_start: 0.5897 (m-80) cc_final: 0.5656 (m-80) REVERT: B 238 MET cc_start: 0.6444 (tpp) cc_final: 0.5696 (tpp) REVERT: D 94 LEU cc_start: 0.7970 (mt) cc_final: 0.7650 (mt) REVERT: E 250 TRP cc_start: 0.6737 (OUTLIER) cc_final: 0.6404 (p-90) REVERT: E 265 LEU cc_start: 0.8062 (tp) cc_final: 0.7745 (tp) REVERT: F 95 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6251 (tm-30) REVERT: F 238 MET cc_start: 0.7006 (tpp) cc_final: 0.6703 (tpt) REVERT: F 277 LYS cc_start: 0.6729 (mptt) cc_final: 0.5530 (mptt) outliers start: 66 outliers final: 53 residues processed: 398 average time/residue: 0.2406 time to fit residues: 137.2042 Evaluate side-chains 397 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 342 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13428 Z= 0.304 Angle : 0.676 10.197 18199 Z= 0.345 Chirality : 0.045 0.199 2087 Planarity : 0.005 0.063 2354 Dihedral : 4.870 62.617 1820 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.30 % Allowed : 21.37 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1649 helix: 1.32 (0.24), residues: 472 sheet: -0.64 (0.26), residues: 372 loop : -0.33 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 19 HIS 0.005 0.001 HIS E 22 PHE 0.037 0.002 PHE D 40 TYR 0.023 0.002 TYR B 156 ARG 0.011 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 365 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.5892 (m-80) cc_final: 0.5634 (m-80) REVERT: B 238 MET cc_start: 0.6467 (tpp) cc_final: 0.6144 (tpp) REVERT: F 297 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6176 (mm) outliers start: 94 outliers final: 66 residues processed: 417 average time/residue: 0.2418 time to fit residues: 144.2264 Evaluate side-chains 400 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 333 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 0.0000 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 61 ASN C 115 HIS E 21 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13428 Z= 0.197 Angle : 0.639 10.459 18199 Z= 0.325 Chirality : 0.044 0.183 2087 Planarity : 0.004 0.058 2354 Dihedral : 4.555 61.064 1820 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.95 % Allowed : 25.39 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1649 helix: 1.27 (0.24), residues: 471 sheet: -0.63 (0.25), residues: 405 loop : -0.29 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 19 HIS 0.018 0.001 HIS C 22 PHE 0.034 0.002 PHE D 40 TYR 0.021 0.002 TYR C 40 ARG 0.006 0.001 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 371 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASP cc_start: 0.7454 (p0) cc_final: 0.6823 (p0) REVERT: B 40 PHE cc_start: 0.5855 (m-80) cc_final: 0.5563 (m-80) REVERT: B 238 MET cc_start: 0.6668 (tpp) cc_final: 0.5772 (tpp) REVERT: D 99 LEU cc_start: 0.8142 (tt) cc_final: 0.7817 (tt) REVERT: D 238 MET cc_start: 0.4871 (tpt) cc_final: 0.4389 (tpt) outliers start: 59 outliers final: 47 residues processed: 405 average time/residue: 0.2439 time to fit residues: 141.9152 Evaluate side-chains 393 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 346 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13428 Z= 0.231 Angle : 0.648 9.524 18199 Z= 0.331 Chirality : 0.045 0.207 2087 Planarity : 0.005 0.058 2354 Dihedral : 4.661 60.434 1820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.55 % Allowed : 24.58 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1649 helix: 1.29 (0.24), residues: 471 sheet: -0.59 (0.26), residues: 394 loop : -0.34 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 19 HIS 0.013 0.001 HIS C 22 PHE 0.031 0.002 PHE D 40 TYR 0.032 0.002 TYR E 59 ARG 0.012 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 348 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.5891 (m-80) cc_final: 0.5634 (m-80) REVERT: B 238 MET cc_start: 0.6740 (tpp) cc_final: 0.5891 (tpp) REVERT: D 134 LEU cc_start: 0.5864 (tp) cc_final: 0.5650 (tp) REVERT: D 238 MET cc_start: 0.4725 (tpt) cc_final: 0.4270 (tpt) outliers start: 68 outliers final: 59 residues processed: 385 average time/residue: 0.2330 time to fit residues: 130.8149 Evaluate side-chains 396 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13428 Z= 0.191 Angle : 0.652 10.591 18199 Z= 0.327 Chirality : 0.044 0.173 2087 Planarity : 0.004 0.061 2354 Dihedral : 4.498 59.486 1820 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.55 % Allowed : 25.92 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1649 helix: 1.25 (0.24), residues: 470 sheet: -0.53 (0.26), residues: 401 loop : -0.35 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 250 HIS 0.013 0.001 HIS A 22 PHE 0.031 0.001 PHE D 40 TYR 0.032 0.002 TYR E 59 ARG 0.013 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 356 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.6040 (m-80) cc_final: 0.5719 (m-80) REVERT: B 238 MET cc_start: 0.6598 (tpp) cc_final: 0.5716 (tpp) REVERT: D 238 MET cc_start: 0.4723 (tpt) cc_final: 0.4281 (tpt) outliers start: 53 outliers final: 45 residues processed: 383 average time/residue: 0.2411 time to fit residues: 133.2664 Evaluate side-chains 383 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 338 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 0.0970 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13428 Z= 0.184 Angle : 0.645 9.523 18199 Z= 0.327 Chirality : 0.044 0.235 2087 Planarity : 0.004 0.057 2354 Dihedral : 4.428 59.356 1820 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.42 % Allowed : 26.52 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1649 helix: 1.12 (0.24), residues: 473 sheet: -0.51 (0.26), residues: 406 loop : -0.42 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 250 HIS 0.011 0.001 HIS A 22 PHE 0.030 0.001 PHE D 40 TYR 0.040 0.002 TYR B 66 ARG 0.018 0.001 ARG C 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 358 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASP cc_start: 0.7498 (p0) cc_final: 0.6817 (p0) REVERT: B 40 PHE cc_start: 0.6002 (m-80) cc_final: 0.5698 (m-80) REVERT: B 238 MET cc_start: 0.6539 (tpp) cc_final: 0.5710 (tpp) REVERT: F 41 GLU cc_start: 0.7424 (pp20) cc_final: 0.7082 (pp20) REVERT: F 238 MET cc_start: 0.6781 (tpt) cc_final: 0.6133 (tpt) outliers start: 51 outliers final: 44 residues processed: 388 average time/residue: 0.2369 time to fit residues: 133.2671 Evaluate side-chains 379 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 0.0470 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.220039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176806 restraints weight = 21416.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181863 restraints weight = 12464.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.184267 restraints weight = 9138.064| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13428 Z= 0.196 Angle : 0.659 8.867 18199 Z= 0.333 Chirality : 0.044 0.199 2087 Planarity : 0.004 0.057 2354 Dihedral : 4.411 58.848 1820 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.35 % Allowed : 26.32 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1649 helix: 1.07 (0.24), residues: 473 sheet: -0.49 (0.26), residues: 394 loop : -0.40 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 250 HIS 0.012 0.001 HIS A 22 PHE 0.028 0.002 PHE D 40 TYR 0.051 0.002 TYR B 66 ARG 0.008 0.001 ARG C 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.81 seconds wall clock time: 60 minutes 42.64 seconds (3642.64 seconds total)