Starting phenix.real_space_refine on Thu Mar 14 14:33:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jz7_36736/03_2024/8jz7_36736_neut_updated.pdb" } resolution = 2.6 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= 0.022 sd= 0.118 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 69 5.16 5 C 5765 2.51 5 N 1542 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9042 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1805 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.58 Number of scatterers: 9042 At special positions: 0 Unit cell: (99.36, 138, 120.52, 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 69 16.00 O 1666 8.00 N 1542 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.06 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 2.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 29.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.322A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.551A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 31 removed outlier: 4.018A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 272 through 279 removed outlier: 4.171A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.735A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 4.080A pdb=" N VAL D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.868A pdb=" N LEU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.514A pdb=" N LEU A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 98 through 110 removed outlier: 5.212A pdb=" N MET A 103 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 104 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 109 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.588A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 4.404A pdb=" N ARG A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 188 through 217 removed outlier: 3.514A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.781A pdb=" N ARG A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.681A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.559A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.418A pdb=" N SER A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 277 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Proline residue: A 291 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.735A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.175A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.909A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.585A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.803A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.654A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.635A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.692A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS D 195 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU D 36 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS D 197 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU D 38 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE D 199 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N GLY D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.988A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.336A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.196A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 888 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: 2.22 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2467 1.33 - 1.46: 2674 1.46 - 1.59: 3998 1.59 - 1.72: 0 1.72 - 1.85: 100 Bond restraints: 9239 Sorted by residual: bond pdb=" C GLU S 234 " pdb=" N TYR S 235 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.19e+01 bond pdb=" C04 FI7 A 401 " pdb=" C05 FI7 A 401 " ideal model delta sigma weight residual 1.483 1.390 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" N ARG B 22 " pdb=" CA ARG B 22 " ideal model delta sigma weight residual 1.457 1.516 -0.059 1.33e-02 5.65e+03 1.98e+01 bond pdb=" C20 FI7 A 401 " pdb=" N19 FI7 A 401 " ideal model delta sigma weight residual 1.396 1.327 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C22 FI7 A 401 " pdb=" O23 FI7 A 401 " ideal model delta sigma weight residual 1.269 1.203 0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 9234 not shown) Histogram of bond angle deviations from ideal: 96.54 - 104.23: 102 104.23 - 111.93: 4377 111.93 - 119.63: 3388 119.63 - 127.33: 4533 127.33 - 135.03: 100 Bond angle restraints: 12500 Sorted by residual: angle pdb=" C ARG B 22 " pdb=" N LYS B 23 " pdb=" CA LYS B 23 " ideal model delta sigma weight residual 120.31 112.73 7.58 1.52e+00 4.33e-01 2.48e+01 angle pdb=" C GLU A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta sigma weight residual 122.09 114.17 7.92 1.79e+00 3.12e-01 1.96e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.97 108.32 4.65 1.06e+00 8.90e-01 1.92e+01 angle pdb=" O ALA B 21 " pdb=" C ALA B 21 " pdb=" N ARG B 22 " ideal model delta sigma weight residual 122.27 116.96 5.31 1.23e+00 6.61e-01 1.87e+01 angle pdb=" N ASP D 328 " pdb=" CA ASP D 328 " pdb=" C ASP D 328 " ideal model delta sigma weight residual 108.60 114.57 -5.97 1.46e+00 4.69e-01 1.67e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 4789 15.05 - 30.09: 546 30.09 - 45.14: 121 45.14 - 60.18: 22 60.18 - 75.23: 12 Dihedral angle restraints: 5490 sinusoidal: 2178 harmonic: 3312 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ALA A 174 " pdb=" C ALA A 174 " pdb=" N ASN A 175 " pdb=" CA ASN A 175 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA MET C 21 " pdb=" C MET C 21 " pdb=" N GLU C 22 " pdb=" CA GLU C 22 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 832 0.040 - 0.079: 391 0.079 - 0.119: 139 0.119 - 0.158: 33 0.158 - 0.198: 3 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA ILE D 303 " pdb=" N ILE D 303 " pdb=" C ILE D 303 " pdb=" CB ILE D 303 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CB ILE A 13 " pdb=" CA ILE A 13 " pdb=" CG1 ILE A 13 " pdb=" CG2 ILE A 13 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1395 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 FI7 A 401 " -0.078 2.00e-02 2.50e+03 6.24e-02 6.82e+01 pdb=" C05 FI7 A 401 " 0.031 2.00e-02 2.50e+03 pdb=" C07 FI7 A 401 " 0.062 2.00e-02 2.50e+03 pdb=" C08 FI7 A 401 " -0.096 2.00e-02 2.50e+03 pdb=" N06 FI7 A 401 " 0.083 2.00e-02 2.50e+03 pdb=" N15 FI7 A 401 " 0.011 2.00e-02 2.50e+03 pdb=" O16 FI7 A 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 A 401 " 0.081 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" C08 FI7 A 401 " -0.040 2.00e-02 2.50e+03 pdb=" C09 FI7 A 401 " -0.032 2.00e-02 2.50e+03 pdb=" C10 FI7 A 401 " -0.010 2.00e-02 2.50e+03 pdb=" C11 FI7 A 401 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 A 401 " -0.014 2.00e-02 2.50e+03 pdb=" N14 FI7 A 401 " -0.036 2.00e-02 2.50e+03 pdb=" O12 FI7 A 401 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO S 75 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.037 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 877 2.74 - 3.28: 8901 3.28 - 3.82: 14286 3.82 - 4.36: 17653 4.36 - 4.90: 30134 Nonbonded interactions: 71851 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.206 2.440 nonbonded pdb=" O TRP A 59 " pdb=" ND2 ASN A 141 " model vdw 2.221 2.520 nonbonded pdb=" O THR D 262 " pdb=" NZ LYS D 317 " model vdw 2.222 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.247 2.440 ... (remaining 71846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.750 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: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.006 0.097 9239 Z= 0.393 Angle : 0.852 7.917 12500 Z= 0.489 Chirality : 0.051 0.198 1398 Planarity : 0.005 0.066 1580 Dihedral : 13.847 75.228 3338 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.61 % Allowed : 0.61 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1130 helix: -0.99 (0.28), residues: 335 sheet: -0.19 (0.29), residues: 299 loop : -2.56 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 82 HIS 0.012 0.002 HIS B 54 PHE 0.031 0.003 PHE A 52 TYR 0.033 0.003 TYR S 190 ARG 0.007 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: D 315 ASP cc_start: 0.7065 (p0) cc_final: 0.6860 (p0) REVERT: A 295 TYR cc_start: 0.6748 (m-80) cc_final: 0.5974 (m-80) outliers start: 6 outliers final: 1 residues processed: 184 average time/residue: 1.2509 time to fit residues: 244.7382 Evaluate side-chains 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9239 Z= 0.326 Angle : 0.740 11.662 12500 Z= 0.381 Chirality : 0.048 0.226 1398 Planarity : 0.005 0.064 1580 Dihedral : 7.101 57.658 1265 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.74 % Allowed : 15.62 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.85 (0.24), residues: 1130 helix: -0.56 (0.29), residues: 333 sheet: -0.11 (0.30), residues: 300 loop : -2.43 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 82 HIS 0.010 0.002 HIS B 54 PHE 0.029 0.003 PHE A 117 TYR 0.015 0.002 TYR D 320 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7373 (mpp80) REVERT: B 78 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6216 (mppt) REVERT: S 220 GLU cc_start: 0.7973 (tt0) cc_final: 0.7697 (tt0) REVERT: S 235 TYR cc_start: 0.7902 (m-80) cc_final: 0.7631 (m-80) REVERT: A 234 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6564 (mmt) REVERT: A 295 TYR cc_start: 0.6985 (m-80) cc_final: 0.6415 (m-80) outliers start: 27 outliers final: 13 residues processed: 158 average time/residue: 1.2982 time to fit residues: 217.6976 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 0.0050 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN D 195 HIS ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9239 Z= 0.183 Angle : 0.630 11.347 12500 Z= 0.323 Chirality : 0.044 0.185 1398 Planarity : 0.004 0.063 1580 Dihedral : 6.567 55.963 1263 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.64 % Allowed : 18.97 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.52 (0.25), residues: 1130 helix: -0.11 (0.30), residues: 333 sheet: -0.10 (0.30), residues: 305 loop : -2.26 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.015 0.002 PHE A 74 TYR 0.009 0.001 TYR S 59 ARG 0.002 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7361 (mpp80) REVERT: B 76 ASP cc_start: 0.6450 (t0) cc_final: 0.6107 (t0) REVERT: B 78 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6117 (mppt) REVERT: D 53 MET cc_start: 0.6297 (mtt) cc_final: 0.6014 (mmm) REVERT: D 315 ASP cc_start: 0.7066 (p0) cc_final: 0.6842 (p0) REVERT: S 235 TYR cc_start: 0.7709 (m-80) cc_final: 0.7284 (m-80) REVERT: A 40 PHE cc_start: 0.6371 (m-10) cc_final: 0.6150 (m-80) REVERT: A 234 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6586 (mmt) REVERT: A 295 TYR cc_start: 0.6969 (m-80) cc_final: 0.6633 (m-80) outliers start: 26 outliers final: 11 residues processed: 168 average time/residue: 1.2604 time to fit residues: 225.5383 Evaluate side-chains 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9239 Z= 0.187 Angle : 0.616 10.701 12500 Z= 0.316 Chirality : 0.044 0.181 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.362 55.025 1263 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.45 % Allowed : 20.59 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.33 (0.25), residues: 1130 helix: 0.17 (0.30), residues: 328 sheet: -0.05 (0.30), residues: 306 loop : -2.18 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.018 0.002 PHE A 117 TYR 0.008 0.001 TYR S 102 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7360 (mpp80) REVERT: B 76 ASP cc_start: 0.6433 (t0) cc_final: 0.5958 (t0) REVERT: B 78 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6158 (mppt) REVERT: D 53 MET cc_start: 0.6279 (mtt) cc_final: 0.5992 (mmm) REVERT: D 229 ASP cc_start: 0.6602 (t70) cc_final: 0.6089 (t0) REVERT: D 331 ASN cc_start: 0.7556 (m-40) cc_final: 0.7258 (m-40) REVERT: S 220 GLU cc_start: 0.8003 (tt0) cc_final: 0.7475 (tt0) REVERT: S 235 TYR cc_start: 0.7705 (m-80) cc_final: 0.7217 (m-80) REVERT: A 234 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6594 (mmt) REVERT: A 295 TYR cc_start: 0.6949 (m-80) cc_final: 0.6680 (m-80) outliers start: 34 outliers final: 15 residues processed: 173 average time/residue: 1.1983 time to fit residues: 221.2170 Evaluate side-chains 163 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS A 110 ASN A 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9239 Z= 0.272 Angle : 0.675 11.263 12500 Z= 0.345 Chirality : 0.046 0.214 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.462 53.523 1263 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.16 % Allowed : 21.40 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.34 (0.25), residues: 1130 helix: 0.11 (0.30), residues: 335 sheet: 0.10 (0.31), residues: 286 loop : -2.21 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 93 HIS 0.006 0.001 HIS A 189 PHE 0.024 0.002 PHE A 296 TYR 0.010 0.002 TYR S 59 ARG 0.004 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7284 (mpp80) REVERT: B 76 ASP cc_start: 0.6508 (t0) cc_final: 0.6194 (t0) REVERT: B 78 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6344 (mppt) REVERT: D 53 MET cc_start: 0.6271 (mtt) cc_final: 0.5962 (mmm) REVERT: S 220 GLU cc_start: 0.7992 (tt0) cc_final: 0.7493 (tt0) REVERT: S 235 TYR cc_start: 0.7684 (m-80) cc_final: 0.7208 (m-80) REVERT: A 26 ILE cc_start: 0.5005 (OUTLIER) cc_final: 0.4709 (mm) REVERT: A 234 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6679 (mmt) REVERT: A 295 TYR cc_start: 0.7074 (m-80) cc_final: 0.6620 (m-80) REVERT: A 296 PHE cc_start: 0.6527 (m-80) cc_final: 0.6213 (m-80) outliers start: 41 outliers final: 21 residues processed: 182 average time/residue: 1.1337 time to fit residues: 220.7107 Evaluate side-chains 172 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9239 Z= 0.203 Angle : 0.642 12.969 12500 Z= 0.323 Chirality : 0.044 0.198 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.224 51.905 1263 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.85 % Allowed : 22.92 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.21 (0.25), residues: 1130 helix: 0.29 (0.30), residues: 333 sheet: 0.05 (0.31), residues: 295 loop : -2.13 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.021 0.002 PHE A 117 TYR 0.010 0.001 TYR S 102 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7286 (mpp80) REVERT: B 76 ASP cc_start: 0.6397 (t0) cc_final: 0.6092 (t0) REVERT: B 78 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6309 (mppt) REVERT: D 4 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6182 (p) REVERT: D 53 MET cc_start: 0.6185 (mtt) cc_final: 0.5861 (mmm) REVERT: D 229 ASP cc_start: 0.6565 (t70) cc_final: 0.6058 (t0) REVERT: D 331 ASN cc_start: 0.7520 (m-40) cc_final: 0.7208 (m-40) REVERT: S 21 SER cc_start: 0.7597 (p) cc_final: 0.7217 (t) REVERT: A 198 PHE cc_start: 0.5600 (m-10) cc_final: 0.5361 (m-80) REVERT: A 295 TYR cc_start: 0.7115 (m-80) cc_final: 0.6692 (m-80) REVERT: A 296 PHE cc_start: 0.6496 (m-80) cc_final: 0.6255 (m-80) outliers start: 38 outliers final: 17 residues processed: 182 average time/residue: 1.0908 time to fit residues: 212.7779 Evaluate side-chains 168 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 195 HIS A 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9239 Z= 0.162 Angle : 0.611 11.297 12500 Z= 0.308 Chirality : 0.043 0.149 1398 Planarity : 0.004 0.061 1580 Dihedral : 5.919 48.675 1263 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.55 % Allowed : 24.04 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.08 (0.25), residues: 1130 helix: 0.41 (0.30), residues: 333 sheet: 0.07 (0.30), residues: 299 loop : -2.03 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.024 0.002 PHE A 74 TYR 0.013 0.001 TYR S 102 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7257 (mpp80) REVERT: D 4 THR cc_start: 0.6475 (OUTLIER) cc_final: 0.6220 (p) REVERT: D 53 MET cc_start: 0.6133 (mtt) cc_final: 0.5795 (mmm) REVERT: D 229 ASP cc_start: 0.6556 (t70) cc_final: 0.6059 (t0) REVERT: D 331 ASN cc_start: 0.7310 (m-40) cc_final: 0.7066 (m-40) REVERT: S 21 SER cc_start: 0.7289 (p) cc_final: 0.7032 (t) REVERT: S 220 GLU cc_start: 0.8008 (tt0) cc_final: 0.7729 (mp0) REVERT: A 295 TYR cc_start: 0.7038 (m-80) cc_final: 0.6567 (m-80) REVERT: A 296 PHE cc_start: 0.6543 (m-80) cc_final: 0.6301 (m-80) outliers start: 35 outliers final: 16 residues processed: 189 average time/residue: 1.0385 time to fit residues: 210.8339 Evaluate side-chains 166 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 195 HIS A 171 ASN A 217 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9239 Z= 0.239 Angle : 0.674 12.643 12500 Z= 0.338 Chirality : 0.046 0.321 1398 Planarity : 0.004 0.062 1580 Dihedral : 5.970 45.598 1263 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.75 % Allowed : 25.46 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.13 (0.25), residues: 1130 helix: 0.33 (0.30), residues: 334 sheet: 0.15 (0.30), residues: 291 loop : -2.09 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.024 0.002 PHE S 239 TYR 0.012 0.002 TYR B 59 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7283 (mpp80) REVERT: B 59 TYR cc_start: 0.7220 (m-80) cc_final: 0.6977 (m-80) REVERT: D 4 THR cc_start: 0.6496 (OUTLIER) cc_final: 0.6245 (p) REVERT: D 53 MET cc_start: 0.6148 (mtt) cc_final: 0.5824 (mmm) REVERT: D 229 ASP cc_start: 0.6531 (t70) cc_final: 0.6006 (t0) REVERT: S 21 SER cc_start: 0.7381 (p) cc_final: 0.7082 (t) REVERT: S 220 GLU cc_start: 0.8008 (tt0) cc_final: 0.7732 (mp0) REVERT: A 198 PHE cc_start: 0.5631 (m-10) cc_final: 0.5389 (m-80) REVERT: A 273 ASP cc_start: 0.7976 (m-30) cc_final: 0.7390 (m-30) outliers start: 37 outliers final: 21 residues processed: 182 average time/residue: 1.0357 time to fit residues: 202.8221 Evaluate side-chains 175 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS S 232 HIS A 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9239 Z= 0.180 Angle : 0.636 11.581 12500 Z= 0.317 Chirality : 0.044 0.250 1398 Planarity : 0.004 0.061 1580 Dihedral : 5.756 42.076 1263 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.14 % Allowed : 25.76 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.05 (0.25), residues: 1130 helix: 0.40 (0.30), residues: 332 sheet: 0.07 (0.30), residues: 299 loop : -1.97 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.025 0.002 PHE A 74 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7278 (mpp80) REVERT: D 4 THR cc_start: 0.6519 (OUTLIER) cc_final: 0.6280 (p) REVERT: D 53 MET cc_start: 0.6116 (mtt) cc_final: 0.5784 (mmm) REVERT: D 229 ASP cc_start: 0.6562 (t70) cc_final: 0.6061 (t0) REVERT: D 331 ASN cc_start: 0.7357 (m-40) cc_final: 0.7056 (m-40) REVERT: S 21 SER cc_start: 0.7219 (p) cc_final: 0.7016 (t) REVERT: S 220 GLU cc_start: 0.8011 (tt0) cc_final: 0.7720 (mp0) REVERT: A 273 ASP cc_start: 0.7906 (m-30) cc_final: 0.7295 (m-30) outliers start: 31 outliers final: 21 residues processed: 172 average time/residue: 1.1442 time to fit residues: 211.2394 Evaluate side-chains 172 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 195 HIS A 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9239 Z= 0.272 Angle : 0.693 13.173 12500 Z= 0.348 Chirality : 0.047 0.333 1398 Planarity : 0.004 0.062 1580 Dihedral : 5.932 41.534 1263 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.64 % Allowed : 26.27 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.19 (0.25), residues: 1130 helix: 0.24 (0.30), residues: 333 sheet: 0.15 (0.30), residues: 291 loop : -2.10 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 93 HIS 0.006 0.001 HIS A 189 PHE 0.024 0.002 PHE S 239 TYR 0.009 0.002 TYR D 320 ARG 0.003 0.000 ARG D 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (mpp80) REVERT: D 53 MET cc_start: 0.6207 (mtt) cc_final: 0.5884 (mmm) REVERT: D 229 ASP cc_start: 0.6531 (t70) cc_final: 0.5992 (t0) REVERT: S 21 SER cc_start: 0.7291 (p) cc_final: 0.7011 (t) REVERT: A 198 PHE cc_start: 0.5621 (m-10) cc_final: 0.5385 (m-80) REVERT: A 273 ASP cc_start: 0.7995 (m-30) cc_final: 0.7384 (m-30) outliers start: 26 outliers final: 20 residues processed: 168 average time/residue: 1.1144 time to fit residues: 200.6035 Evaluate side-chains 164 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.151137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.128350 restraints weight = 15114.236| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.09 r_work: 0.3878 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9239 Z= 0.229 Angle : 0.672 11.654 12500 Z= 0.337 Chirality : 0.046 0.305 1398 Planarity : 0.004 0.061 1580 Dihedral : 5.834 39.537 1263 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.84 % Allowed : 25.96 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.16 (0.25), residues: 1130 helix: 0.22 (0.30), residues: 334 sheet: 0.13 (0.30), residues: 291 loop : -2.04 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.025 0.002 PHE S 239 TYR 0.008 0.001 TYR D 320 ARG 0.003 0.000 ARG D 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.91 seconds wall clock time: 74 minutes 29.90 seconds (4469.90 seconds total)