Starting phenix.real_space_refine on Wed Feb 14 20:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysf_10895/02_2024/6ysf_10895.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 95 5.16 5 C 6543 2.51 5 N 1674 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 242": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10220 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "E" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "C" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Time building chain proxies: 5.84, per 1000 atoms: 0.57 Number of scatterers: 10220 At special positions: 0 Unit cell: (94.53, 114.258, 103.572, 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 95 16.00 O 1908 8.00 N 1674 7.00 C 6543 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: 4.63 Conformation dependent library (CDL) restraints added in 2.0 seconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 Processing helix chain 'B' and resid 17 through 43 removed outlier: 3.884A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 25 removed outlier: 4.406A pdb=" N VAL E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.604A pdb=" N VAL E 32 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 34 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.682A pdb=" N VAL E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.692A pdb=" N GLN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.835A pdb=" N MET E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 173 removed outlier: 4.135A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Proline residue: E 157 - end of helix removed outlier: 3.679A pdb=" N GLN E 170 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 202 removed outlier: 3.721A pdb=" N MET E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 232 Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.591A pdb=" N SER E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 removed outlier: 3.617A pdb=" N LYS E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.725A pdb=" N VAL C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 19 " --> pdb=" O CYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 62 through 71 removed outlier: 4.908A pdb=" N GLN C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.946A pdb=" N GLN C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 removed outlier: 3.762A pdb=" N GLY C 114 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 172 removed outlier: 3.519A pdb=" N ILE C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.438A pdb=" N SER C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix removed outlier: 4.536A pdb=" N GLY C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.509A pdb=" N GLN C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.523A pdb=" N CYS D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 removed outlier: 4.134A pdb=" N VAL D 32 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP D 34 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 54 Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.785A pdb=" N LEU D 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 64 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 removed outlier: 4.014A pdb=" N PHE D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.608A pdb=" N LYS D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.695A pdb=" N ASN D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 123 through 172 removed outlier: 3.921A pdb=" N ILE D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.798A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 233 removed outlier: 4.032A pdb=" N MET D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.875A pdb=" N GLU D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 249 through 257 removed outlier: 4.375A pdb=" N GLN D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 22 removed outlier: 3.548A pdb=" N ILE F 10 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 26 removed outlier: 4.208A pdb=" N GLY F 26 " --> pdb=" O MET F 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 23 through 26' Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.617A pdb=" N PHE F 33 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 54 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 66 through 72 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.194A pdb=" N LEU F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.651A pdb=" N LYS F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 174 removed outlier: 3.525A pdb=" N GLU F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Proline residue: F 157 - end of helix removed outlier: 3.910A pdb=" N ASN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 202 removed outlier: 3.524A pdb=" N ALA F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 234 removed outlier: 3.535A pdb=" N MET F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 245 removed outlier: 3.626A pdb=" N GLU F 241 " --> pdb=" O PRO F 237 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 244 " --> pdb=" O MET F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.905A pdb=" N GLN F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.795A pdb=" N LEU G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 22 " --> pdb=" O LEU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.077A pdb=" N VAL G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 3.539A pdb=" N GLN G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 90 removed outlier: 4.255A pdb=" N ILE G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 125 through 171 Proline residue: G 157 - end of helix removed outlier: 3.783A pdb=" N MET G 171 " --> pdb=" O GLY G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 4.576A pdb=" N THR G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN G 204 " --> pdb=" O ASN G 200 " (cutoff:3.500A) Proline residue: G 205 - end of helix removed outlier: 3.670A pdb=" N SER G 233 " --> pdb=" O LEU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 249 through 259 removed outlier: 4.109A pdb=" N LYS G 258 " --> pdb=" O GLN G 254 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 4.97 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: 3280 1.34 - 1.46: 2155 1.46 - 1.58: 4767 1.58 - 1.70: 0 1.70 - 1.81: 185 Bond restraints: 10387 Sorted by residual: bond pdb=" N ILE F 135 " pdb=" CA ILE F 135 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.61e+00 bond pdb=" N LYS F 113 " pdb=" CA LYS F 113 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.41e+00 bond pdb=" N ARG C 238 " pdb=" CA ARG C 238 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N LEU F 133 " pdb=" CA LEU F 133 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.33e+00 bond pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.25e-02 6.40e+03 5.28e+00 ... (remaining 10382 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.55: 219 105.55 - 112.66: 5394 112.66 - 119.78: 3568 119.78 - 126.89: 4730 126.89 - 134.00: 91 Bond angle restraints: 14002 Sorted by residual: angle pdb=" N ILE F 78 " pdb=" CA ILE F 78 " pdb=" C ILE F 78 " ideal model delta sigma weight residual 113.71 108.08 5.63 9.50e-01 1.11e+00 3.51e+01 angle pdb=" N ARG F 116 " pdb=" CA ARG F 116 " pdb=" C ARG F 116 " ideal model delta sigma weight residual 111.82 106.55 5.27 1.16e+00 7.43e-01 2.06e+01 angle pdb=" C THR F 107 " pdb=" N ASP F 108 " pdb=" CA ASP F 108 " ideal model delta sigma weight residual 120.82 127.40 -6.58 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ARG E 92 " pdb=" N ARG E 93 " pdb=" CA ARG E 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N ARG C 253 " pdb=" CA ARG C 253 " pdb=" C ARG C 253 " ideal model delta sigma weight residual 111.82 107.48 4.34 1.16e+00 7.43e-01 1.40e+01 ... (remaining 13997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5511 17.91 - 35.81: 616 35.81 - 53.72: 106 53.72 - 71.62: 19 71.62 - 89.53: 9 Dihedral angle restraints: 6261 sinusoidal: 2501 harmonic: 3760 Sorted by residual: dihedral pdb=" CA ASP F 108 " pdb=" C ASP F 108 " pdb=" N ASP F 109 " pdb=" CA ASP F 109 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP E 108 " pdb=" C ASP E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN G 236 " pdb=" C ASN G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1069 0.040 - 0.079: 435 0.079 - 0.119: 99 0.119 - 0.158: 10 0.158 - 0.198: 5 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CA ILE F 135 " pdb=" N ILE F 135 " pdb=" C ILE F 135 " pdb=" CB ILE F 135 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA LEU F 133 " pdb=" N LEU F 133 " pdb=" C LEU F 133 " pdb=" CB LEU F 133 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA ARG F 116 " pdb=" N ARG F 116 " pdb=" C ARG F 116 " pdb=" CB ARG F 116 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1615 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 236 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO G 237 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 237 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 115 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU F 115 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU F 115 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG F 116 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 41 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C ILE D 41 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE D 41 " -0.011 2.00e-02 2.50e+03 pdb=" N THR D 42 " -0.010 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 56 2.48 - 3.08: 7683 3.08 - 3.69: 15875 3.69 - 4.29: 22858 4.29 - 4.90: 37509 Nonbonded interactions: 83981 Sorted by model distance: nonbonded pdb=" NH2 ARG C 238 " pdb=" OD2 ASP D 120 " model vdw 1.874 2.520 nonbonded pdb=" OE2 GLU C 242 " pdb=" NZ LYS D 113 " model vdw 1.893 2.520 nonbonded pdb=" NZ LYS D 113 " pdb=" OE2 GLU D 134 " model vdw 2.012 2.520 nonbonded pdb=" CE LYS D 113 " pdb=" OE2 GLU D 134 " model vdw 2.041 3.440 nonbonded pdb=" O ALA E 49 " pdb=" OG1 THR E 53 " model vdw 2.122 2.440 ... (remaining 83976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 42) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 8 through 259) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.150 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.210 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10387 Z= 0.267 Angle : 0.765 8.602 14002 Z= 0.452 Chirality : 0.043 0.198 1618 Planarity : 0.005 0.053 1764 Dihedral : 15.307 89.525 3853 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.90 % Allowed : 6.21 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), residues: 1313 helix: -1.53 (0.15), residues: 946 sheet: None (None), residues: 0 loop : -3.91 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS F 142 PHE 0.011 0.001 PHE D 212 TYR 0.011 0.002 TYR G 155 ARG 0.005 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 365 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: E 79 ASP cc_start: 0.5379 (t0) cc_final: 0.5156 (t0) REVERT: E 124 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7184 (Cg_endo) REVERT: E 131 MET cc_start: 0.7107 (mmt) cc_final: 0.6810 (mmt) REVERT: E 139 GLU cc_start: 0.6281 (mt-10) cc_final: 0.6002 (mt-10) REVERT: E 236 ASN cc_start: 0.7773 (p0) cc_final: 0.7527 (p0) REVERT: E 240 MET cc_start: 0.7599 (tmm) cc_final: 0.6962 (tmm) REVERT: C 113 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7229 (ttpt) REVERT: C 185 MET cc_start: 0.7195 (mtp) cc_final: 0.6957 (mtp) REVERT: C 242 GLU cc_start: 0.6484 (tp30) cc_final: 0.6236 (tp30) REVERT: C 254 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: D 71 LYS cc_start: 0.6348 (pttt) cc_final: 0.6034 (pttt) REVERT: D 82 GLN cc_start: 0.7808 (mt0) cc_final: 0.7576 (tt0) REVERT: D 112 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7351 (mtmt) REVERT: F 112 LYS cc_start: 0.7855 (mttt) cc_final: 0.7157 (tmtt) REVERT: G 57 ASP cc_start: 0.7552 (t70) cc_final: 0.7341 (t0) REVERT: G 71 LYS cc_start: 0.7383 (mttm) cc_final: 0.7086 (mtmt) REVERT: G 75 MET cc_start: 0.4236 (mmm) cc_final: 0.3700 (mmt) REVERT: G 111 MET cc_start: 0.6719 (mpp) cc_final: 0.6356 (mpp) REVERT: G 131 MET cc_start: 0.5546 (mmp) cc_final: 0.5137 (mtp) outliers start: 10 outliers final: 3 residues processed: 371 average time/residue: 0.2499 time to fit residues: 124.0342 Evaluate side-chains 289 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 284 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 232 GLN C 77 ASN C 204 ASN D 170 GLN F 105 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10387 Z= 0.275 Angle : 0.686 12.951 14002 Z= 0.348 Chirality : 0.043 0.195 1618 Planarity : 0.005 0.045 1764 Dihedral : 6.044 69.564 1425 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.34 % Allowed : 18.26 % Favored : 79.41 % 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: -1.82 (0.22), residues: 1313 helix: -0.30 (0.16), residues: 986 sheet: None (None), residues: 0 loop : -3.91 (0.27), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.013 0.002 PHE B 33 TYR 0.020 0.002 TYR E 110 ARG 0.005 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 297 time to evaluate : 1.291 Fit side-chains REVERT: E 124 PRO cc_start: 0.7561 (Cg_exo) cc_final: 0.7223 (Cg_endo) REVERT: E 131 MET cc_start: 0.7533 (mmt) cc_final: 0.7111 (mmt) REVERT: E 213 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7866 (ttpp) REVERT: E 240 MET cc_start: 0.7571 (tmm) cc_final: 0.7205 (tmm) REVERT: C 123 GLU cc_start: 0.6586 (pt0) cc_final: 0.6211 (tt0) REVERT: C 250 PRO cc_start: 0.8151 (Cg_exo) cc_final: 0.7923 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6516 (pp) REVERT: D 113 LYS cc_start: 0.7437 (tmtp) cc_final: 0.6904 (ttpp) REVERT: D 185 MET cc_start: 0.8187 (tpp) cc_final: 0.7926 (tpp) REVERT: F 50 MET cc_start: 0.7994 (mmm) cc_final: 0.7730 (mmm) REVERT: F 112 LYS cc_start: 0.7832 (mttt) cc_final: 0.7122 (tmtt) REVERT: F 222 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7625 (mm-30) REVERT: G 50 MET cc_start: 0.8608 (mmm) cc_final: 0.8049 (mmm) REVERT: G 57 ASP cc_start: 0.7706 (t70) cc_final: 0.7466 (t0) REVERT: G 71 LYS cc_start: 0.7370 (mttm) cc_final: 0.7053 (mtmt) REVERT: G 75 MET cc_start: 0.4529 (mmm) cc_final: 0.3674 (mmt) REVERT: G 111 MET cc_start: 0.6742 (mpp) cc_final: 0.6405 (mpp) REVERT: G 131 MET cc_start: 0.5637 (mmp) cc_final: 0.5080 (mtp) outliers start: 26 outliers final: 14 residues processed: 310 average time/residue: 0.2216 time to fit residues: 95.7176 Evaluate side-chains 283 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 268 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 174 ASN D 170 GLN F 170 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10387 Z= 0.190 Angle : 0.624 14.277 14002 Z= 0.318 Chirality : 0.041 0.197 1618 Planarity : 0.005 0.044 1764 Dihedral : 5.040 40.250 1412 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.52 % Allowed : 20.95 % Favored : 76.53 % 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: -0.97 (0.23), residues: 1313 helix: 0.32 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -3.66 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 21 HIS 0.001 0.001 HIS F 142 PHE 0.014 0.001 PHE D 203 TYR 0.018 0.002 TYR G 155 ARG 0.005 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 PRO cc_start: 0.7581 (Cg_exo) cc_final: 0.7129 (Cg_endo) REVERT: E 240 MET cc_start: 0.7686 (tmm) cc_final: 0.7361 (tmm) REVERT: C 47 MET cc_start: 0.7819 (mmm) cc_final: 0.7533 (mmm) REVERT: C 252 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6729 (mt-10) REVERT: D 62 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6533 (pp) REVERT: D 113 LYS cc_start: 0.7496 (tmtp) cc_final: 0.6899 (tmtp) REVERT: D 185 MET cc_start: 0.8107 (tpp) cc_final: 0.7886 (tpp) REVERT: D 238 ARG cc_start: 0.7714 (mmp-170) cc_final: 0.7442 (mmm160) REVERT: F 23 MET cc_start: 0.6926 (mpp) cc_final: 0.6336 (mpp) REVERT: F 75 MET cc_start: 0.5819 (ptm) cc_final: 0.5291 (mmm) REVERT: F 112 LYS cc_start: 0.7824 (tttt) cc_final: 0.7041 (tmtt) REVERT: G 33 PHE cc_start: 0.7942 (m-80) cc_final: 0.7243 (m-80) REVERT: G 50 MET cc_start: 0.8530 (mmm) cc_final: 0.8001 (mmm) REVERT: G 75 MET cc_start: 0.4546 (mmm) cc_final: 0.3809 (mmt) REVERT: G 111 MET cc_start: 0.6625 (mpp) cc_final: 0.6363 (mpp) REVERT: G 131 MET cc_start: 0.5341 (mmp) cc_final: 0.4890 (mtp) outliers start: 28 outliers final: 19 residues processed: 330 average time/residue: 0.2202 time to fit residues: 100.6880 Evaluate side-chains 285 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN D 170 GLN F 170 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10387 Z= 0.272 Angle : 0.671 14.577 14002 Z= 0.339 Chirality : 0.043 0.196 1618 Planarity : 0.005 0.046 1764 Dihedral : 5.086 38.325 1412 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.78 % Allowed : 22.21 % Favored : 74.01 % 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: -0.86 (0.23), residues: 1313 helix: 0.38 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -3.47 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.016 0.002 PHE G 212 TYR 0.017 0.002 TYR C 110 ARG 0.005 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 1.231 Fit side-chains REVERT: E 240 MET cc_start: 0.7817 (tmm) cc_final: 0.7487 (tmm) REVERT: C 123 GLU cc_start: 0.6633 (pt0) cc_final: 0.6365 (tt0) REVERT: C 136 ASP cc_start: 0.7427 (m-30) cc_final: 0.7150 (m-30) REVERT: D 62 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6534 (pp) REVERT: D 185 MET cc_start: 0.8197 (tpp) cc_final: 0.7959 (tpp) REVERT: F 23 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6681 (mpp) REVERT: F 112 LYS cc_start: 0.7811 (mttt) cc_final: 0.7103 (tmtt) REVERT: G 50 MET cc_start: 0.8461 (mmm) cc_final: 0.7964 (mmm) REVERT: G 75 MET cc_start: 0.4599 (mmm) cc_final: 0.3870 (mmt) REVERT: G 111 MET cc_start: 0.6627 (mpp) cc_final: 0.6200 (mpp) REVERT: G 131 MET cc_start: 0.5506 (mmp) cc_final: 0.4925 (mtp) outliers start: 42 outliers final: 31 residues processed: 297 average time/residue: 0.2055 time to fit residues: 86.8049 Evaluate side-chains 295 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 170 GLN F 170 GLN G 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10387 Z= 0.175 Angle : 0.613 14.357 14002 Z= 0.312 Chirality : 0.041 0.213 1618 Planarity : 0.005 0.044 1764 Dihedral : 4.806 31.489 1412 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.42 % Allowed : 23.56 % Favored : 73.02 % 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: -0.48 (0.24), residues: 1313 helix: 0.66 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -3.41 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.001 0.000 HIS F 142 PHE 0.014 0.001 PHE D 203 TYR 0.018 0.002 TYR C 155 ARG 0.006 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 311 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6818 (mp) REVERT: E 73 ASN cc_start: 0.7697 (m-40) cc_final: 0.7450 (m110) REVERT: E 94 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6004 (pp20) REVERT: E 161 MET cc_start: 0.7238 (tpp) cc_final: 0.6934 (mpp) REVERT: E 240 MET cc_start: 0.7802 (tmm) cc_final: 0.7460 (tmm) REVERT: E 244 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8620 (mm) REVERT: C 136 ASP cc_start: 0.7475 (m-30) cc_final: 0.7191 (m-30) REVERT: C 241 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6943 (tt0) REVERT: D 113 LYS cc_start: 0.7900 (tttm) cc_final: 0.7643 (ttpp) REVERT: D 132 GLU cc_start: 0.6925 (tp30) cc_final: 0.6713 (tp30) REVERT: F 16 PHE cc_start: 0.7470 (m-80) cc_final: 0.7203 (m-80) REVERT: F 23 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6222 (mpp) REVERT: F 112 LYS cc_start: 0.7777 (mttt) cc_final: 0.7019 (tmtt) REVERT: F 131 MET cc_start: 0.8224 (mmm) cc_final: 0.7717 (mmm) REVERT: G 50 MET cc_start: 0.8398 (mmm) cc_final: 0.7895 (mmm) REVERT: G 75 MET cc_start: 0.4581 (mmm) cc_final: 0.3885 (mmt) REVERT: G 111 MET cc_start: 0.6548 (mpp) cc_final: 0.6239 (mpp) REVERT: G 131 MET cc_start: 0.5304 (mmp) cc_final: 0.5057 (mtt) outliers start: 38 outliers final: 26 residues processed: 327 average time/residue: 0.2081 time to fit residues: 96.2415 Evaluate side-chains 306 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.0570 chunk 66 optimal weight: 6.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 170 GLN F 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10387 Z= 0.168 Angle : 0.641 14.379 14002 Z= 0.320 Chirality : 0.041 0.222 1618 Planarity : 0.005 0.054 1764 Dihedral : 4.687 29.360 1412 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.78 % Allowed : 25.00 % Favored : 71.22 % 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: -0.20 (0.24), residues: 1313 helix: 0.89 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -3.28 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 21 HIS 0.002 0.000 HIS G 142 PHE 0.042 0.002 PHE B 33 TYR 0.031 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 310 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6812 (mp) REVERT: E 94 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: E 240 MET cc_start: 0.7787 (tmm) cc_final: 0.7436 (tmm) REVERT: E 244 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (mm) REVERT: C 56 MET cc_start: 0.6042 (mmm) cc_final: 0.5541 (mmt) REVERT: C 136 ASP cc_start: 0.7536 (m-30) cc_final: 0.7248 (m-30) REVERT: C 241 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7096 (tt0) REVERT: D 62 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6557 (pp) REVERT: D 113 LYS cc_start: 0.7886 (tttm) cc_final: 0.7442 (tttm) REVERT: D 132 GLU cc_start: 0.6843 (tp30) cc_final: 0.6557 (tp30) REVERT: F 23 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6370 (mpp) REVERT: F 50 MET cc_start: 0.7733 (mmm) cc_final: 0.7504 (mmm) REVERT: F 75 MET cc_start: 0.5750 (ptm) cc_final: 0.5419 (mmp) REVERT: F 112 LYS cc_start: 0.7749 (mttt) cc_final: 0.6978 (tmtt) REVERT: F 131 MET cc_start: 0.8192 (mmm) cc_final: 0.7710 (mmm) REVERT: G 50 MET cc_start: 0.8331 (mmm) cc_final: 0.7863 (mmm) REVERT: G 111 MET cc_start: 0.6548 (mpp) cc_final: 0.6275 (mpp) REVERT: G 131 MET cc_start: 0.5396 (mmp) cc_final: 0.4951 (mtt) outliers start: 42 outliers final: 28 residues processed: 331 average time/residue: 0.2062 time to fit residues: 96.5182 Evaluate side-chains 312 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 279 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN F 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10387 Z= 0.323 Angle : 0.724 14.449 14002 Z= 0.365 Chirality : 0.046 0.206 1618 Planarity : 0.005 0.045 1764 Dihedral : 5.039 31.211 1412 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.04 % Allowed : 23.65 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1313 helix: 0.58 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -3.30 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 21 HIS 0.003 0.001 HIS G 142 PHE 0.017 0.002 PHE F 33 TYR 0.020 0.003 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5980 (pp20) REVERT: E 240 MET cc_start: 0.7896 (tmm) cc_final: 0.7515 (tmm) REVERT: E 244 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 56 MET cc_start: 0.6125 (mmm) cc_final: 0.5859 (mmt) REVERT: C 123 GLU cc_start: 0.6695 (pt0) cc_final: 0.6401 (tt0) REVERT: C 136 ASP cc_start: 0.7679 (m-30) cc_final: 0.7444 (m-30) REVERT: D 62 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6516 (pp) REVERT: F 23 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6696 (mpp) REVERT: F 112 LYS cc_start: 0.7889 (mttt) cc_final: 0.7167 (tmtt) REVERT: F 131 MET cc_start: 0.8144 (mmm) cc_final: 0.7662 (mmm) REVERT: F 256 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.4409 (p90) REVERT: G 50 MET cc_start: 0.8433 (mmm) cc_final: 0.8013 (mmm) REVERT: G 111 MET cc_start: 0.6463 (mpp) cc_final: 0.6196 (mpp) REVERT: G 131 MET cc_start: 0.5430 (mmp) cc_final: 0.4970 (mtt) outliers start: 56 outliers final: 40 residues processed: 314 average time/residue: 0.1957 time to fit residues: 87.9179 Evaluate side-chains 312 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 267 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 83 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10387 Z= 0.205 Angle : 0.676 14.162 14002 Z= 0.341 Chirality : 0.043 0.220 1618 Planarity : 0.005 0.041 1764 Dihedral : 4.822 29.420 1412 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.05 % Allowed : 25.09 % 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: -0.40 (0.24), residues: 1313 helix: 0.69 (0.17), residues: 977 sheet: None (None), residues: 0 loop : -3.16 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.001 0.001 HIS G 142 PHE 0.016 0.001 PHE D 203 TYR 0.020 0.002 TYR G 155 ARG 0.006 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 277 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5937 (pp20) REVERT: E 240 MET cc_start: 0.7847 (tmm) cc_final: 0.7522 (tmm) REVERT: E 244 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 56 MET cc_start: 0.6271 (mmm) cc_final: 0.6027 (mmt) REVERT: C 136 ASP cc_start: 0.7636 (m-30) cc_final: 0.7384 (m-30) REVERT: D 62 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6560 (pp) REVERT: D 113 LYS cc_start: 0.7839 (tttm) cc_final: 0.7478 (tttm) REVERT: D 132 GLU cc_start: 0.6888 (tp30) cc_final: 0.6688 (tp30) REVERT: D 149 LEU cc_start: 0.8684 (mt) cc_final: 0.8048 (mp) REVERT: F 23 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: F 50 MET cc_start: 0.7648 (mmm) cc_final: 0.7407 (mmm) REVERT: F 112 LYS cc_start: 0.7797 (mttt) cc_final: 0.7046 (tmtt) REVERT: F 131 MET cc_start: 0.8111 (mmm) cc_final: 0.7686 (mmm) REVERT: F 256 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4409 (p90) REVERT: G 50 MET cc_start: 0.8347 (mmm) cc_final: 0.7921 (mmm) REVERT: G 111 MET cc_start: 0.6481 (mpp) cc_final: 0.6228 (mpp) REVERT: G 131 MET cc_start: 0.5270 (mmp) cc_final: 0.4906 (mtt) outliers start: 45 outliers final: 36 residues processed: 304 average time/residue: 0.2078 time to fit residues: 89.5539 Evaluate side-chains 310 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.0000 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 0.0020 chunk 105 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10387 Z= 0.181 Angle : 0.670 14.154 14002 Z= 0.338 Chirality : 0.042 0.256 1618 Planarity : 0.005 0.042 1764 Dihedral : 4.659 29.475 1412 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.78 % Allowed : 25.54 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1313 helix: 0.86 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -3.09 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 21 HIS 0.001 0.000 HIS G 142 PHE 0.014 0.001 PHE D 203 TYR 0.030 0.002 TYR F 155 ARG 0.007 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 298 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5899 (pp20) REVERT: E 172 LEU cc_start: 0.8584 (pp) cc_final: 0.8127 (mt) REVERT: E 240 MET cc_start: 0.7838 (tmm) cc_final: 0.7591 (tmm) REVERT: E 244 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8563 (mm) REVERT: C 136 ASP cc_start: 0.7692 (m-30) cc_final: 0.7436 (m-30) REVERT: D 62 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6587 (pp) REVERT: D 113 LYS cc_start: 0.7678 (tttm) cc_final: 0.7372 (tttp) REVERT: D 132 GLU cc_start: 0.6878 (tp30) cc_final: 0.6619 (tp30) REVERT: F 23 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: F 75 MET cc_start: 0.5886 (ptm) cc_final: 0.5242 (mmm) REVERT: F 112 LYS cc_start: 0.7795 (mttt) cc_final: 0.7008 (tmtt) REVERT: F 131 MET cc_start: 0.8094 (mmm) cc_final: 0.7707 (mmm) REVERT: G 50 MET cc_start: 0.8317 (mmm) cc_final: 0.7841 (mmm) REVERT: G 111 MET cc_start: 0.6471 (mpp) cc_final: 0.6181 (mpp) REVERT: G 131 MET cc_start: 0.5079 (mmp) cc_final: 0.4786 (mtt) outliers start: 42 outliers final: 28 residues processed: 323 average time/residue: 0.1901 time to fit residues: 88.7718 Evaluate side-chains 305 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN D 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10387 Z= 0.213 Angle : 0.741 19.370 14002 Z= 0.363 Chirality : 0.043 0.254 1618 Planarity : 0.005 0.041 1764 Dihedral : 4.697 29.705 1412 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.24 % Allowed : 26.08 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1313 helix: 0.83 (0.17), residues: 973 sheet: None (None), residues: 0 loop : -2.99 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.014 0.001 PHE D 203 TYR 0.026 0.002 TYR G 155 ARG 0.008 0.000 ARG D 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 280 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: E 240 MET cc_start: 0.7926 (tmm) cc_final: 0.7653 (tmm) REVERT: E 244 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (mm) REVERT: C 136 ASP cc_start: 0.7660 (m-30) cc_final: 0.7421 (m-30) REVERT: D 62 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6597 (pp) REVERT: F 23 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: F 112 LYS cc_start: 0.7829 (mttt) cc_final: 0.7031 (tmtt) REVERT: F 131 MET cc_start: 0.8094 (mmm) cc_final: 0.7635 (mmm) REVERT: G 50 MET cc_start: 0.8281 (mmm) cc_final: 0.7858 (mmm) REVERT: G 111 MET cc_start: 0.6525 (mpp) cc_final: 0.6222 (mpp) REVERT: G 131 MET cc_start: 0.5165 (mmp) cc_final: 0.4864 (mtt) outliers start: 36 outliers final: 27 residues processed: 300 average time/residue: 0.1981 time to fit residues: 85.1422 Evaluate side-chains 294 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN C 83 ASN D 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137214 restraints weight = 14628.687| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.81 r_work: 0.3632 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10387 Z= 0.199 Angle : 0.734 17.776 14002 Z= 0.361 Chirality : 0.043 0.234 1618 Planarity : 0.005 0.042 1764 Dihedral : 4.653 29.954 1412 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.24 % Allowed : 26.98 % Favored : 69.78 % 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: -0.19 (0.24), residues: 1313 helix: 0.84 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -3.11 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 21 HIS 0.001 0.001 HIS G 142 PHE 0.014 0.001 PHE D 203 TYR 0.029 0.002 TYR D 194 ARG 0.004 0.000 ARG C 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.90 seconds wall clock time: 49 minutes 34.92 seconds (2974.92 seconds total)