Starting phenix.real_space_refine on Tue May 7 20:36:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/05_2024/8x17_37986_updated.pdb" } resolution = 3.19 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= 0.007 sd= 0.087 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 Cl 1 4.86 5 C 5615 2.51 5 N 1469 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R GLU 291": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8753 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2269 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'XS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.56 Number of scatterers: 8753 At special positions: 0 Unit cell: (116.184, 88.992, 135.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 Cl 1 17.00 S 68 16.00 O 1599 8.00 N 1469 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 13 sheets defined 35.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.559A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.964A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 39 Processing helix chain 'R' and resid 41 through 43 No H-bonds generated for 'chain 'R' and resid 41 through 43' Processing helix chain 'R' and resid 46 through 74 removed outlier: 3.501A pdb=" N PHE R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 80 through 113 removed outlier: 3.507A pdb=" N THR R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 121 Processing helix chain 'R' and resid 124 through 145 Proline residue: R 145 - end of helix Processing helix chain 'R' and resid 151 through 153 No H-bonds generated for 'chain 'R' and resid 151 through 153' Processing helix chain 'R' and resid 158 through 160 No H-bonds generated for 'chain 'R' and resid 158 through 160' Processing helix chain 'R' and resid 168 through 171 No H-bonds generated for 'chain 'R' and resid 168 through 171' Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 181 through 185 Processing helix chain 'R' and resid 187 through 208 Processing helix chain 'R' and resid 224 through 252 removed outlier: 3.586A pdb=" N PHE R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 261 through 282 removed outlier: 3.869A pdb=" N ASN R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET R 276 " --> pdb=" O HIS R 272 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 287 through 299 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.509A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.676A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.988A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.811A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.112A 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: 6.718A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.567A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.516A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.358A 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: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.758A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.746A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.941A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.413A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'H' and resid 225 through 231 removed outlier: 3.524A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG H 180 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 319 through 324 removed outlier: 7.093A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1122 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: 2.51 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3333 1.38 - 1.57: 5498 1.57 - 1.75: 3 1.75 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 8937 Sorted by residual: bond pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " ideal model delta sigma weight residual 1.342 1.640 -0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C08 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 1.606 1.322 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C05 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 1.294 1.527 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C06 XS0 R 401 " pdb=" C07 XS0 R 401 " ideal model delta sigma weight residual 1.508 1.289 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C16 XS0 R 401 " pdb="CL19 XS0 R 401 " ideal model delta sigma weight residual 1.785 1.889 -0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.77: 91 103.77 - 111.58: 4232 111.58 - 119.38: 3113 119.38 - 127.19: 4592 127.19 - 135.00: 91 Bond angle restraints: 12119 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 111.45 105.38 6.07 9.30e-01 1.16e+00 4.26e+01 angle pdb=" N10 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 110.36 95.97 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" N10 XS0 R 401 " ideal model delta sigma weight residual 110.37 124.11 -13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C LEU R 84 " pdb=" N PHE R 85 " pdb=" CA PHE R 85 " ideal model delta sigma weight residual 120.31 113.51 6.80 1.52e+00 4.33e-01 2.00e+01 angle pdb=" C SER R 165 " pdb=" N CYS R 166 " pdb=" CA CYS R 166 " ideal model delta sigma weight residual 122.84 117.87 4.97 1.30e+00 5.92e-01 1.46e+01 ... (remaining 12114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4856 17.35 - 34.71: 328 34.71 - 52.06: 64 52.06 - 69.41: 11 69.41 - 86.76: 5 Dihedral angle restraints: 5264 sinusoidal: 1988 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 83 " pdb=" SG CYS R 83 " pdb=" SG CYS R 166 " pdb=" CB CYS R 166 " ideal model delta sinusoidal sigma weight residual -86.00 -136.59 50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " pdb=" OD1 ASP A 261 " ideal model delta sinusoidal sigma weight residual -30.00 -88.10 58.10 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" N LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sinusoidal sigma weight residual -60.00 -117.05 57.05 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1369 0.110 - 0.219: 33 0.219 - 0.329: 0 0.329 - 0.438: 1 0.438 - 0.548: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C05 XS0 R 401 " pdb=" C03 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" O09 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.49 3.04 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C06 XS0 R 401 " pdb=" C05 XS0 R 401 " pdb=" C07 XS0 R 401 " pdb=" O30 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.56 2.21 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1401 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 81 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C TYR R 81 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR R 81 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 250 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ASN R 250 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN R 250 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS R 251 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO H 236 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.63: 116 2.63 - 3.22: 8530 3.22 - 3.80: 14311 3.80 - 4.38: 20171 4.38 - 4.96: 33628 Nonbonded interactions: 76756 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.053 2.440 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.227 2.520 nonbonded pdb=" OE1 GLU A 318 " pdb=" NZ LYS A 345 " model vdw 2.259 2.520 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.269 2.440 ... (remaining 76751 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: 1.320 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: 3.980 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.298 8937 Z= 0.438 Angle : 0.523 14.391 12119 Z= 0.315 Chirality : 0.042 0.548 1404 Planarity : 0.003 0.047 1507 Dihedral : 12.459 86.763 3147 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.31 % 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: -0.96 (0.25), residues: 1109 helix: 0.15 (0.25), residues: 406 sheet: -0.91 (0.29), residues: 273 loop : -1.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 339 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.000 PHE R 48 TYR 0.005 0.000 TYR H 190 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 0.971 Fit side-chains REVERT: B 243 THR cc_start: 0.7925 (p) cc_final: 0.7543 (p) REVERT: R 99 MET cc_start: 0.8433 (mmm) cc_final: 0.8219 (mmm) REVERT: R 288 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7848 (tttp) REVERT: H 59 TYR cc_start: 0.5904 (m-80) cc_final: 0.5632 (m-80) REVERT: H 94 TYR cc_start: 0.8419 (m-80) cc_final: 0.7989 (m-80) REVERT: H 106 SER cc_start: 0.8681 (t) cc_final: 0.8374 (p) REVERT: A 305 CYS cc_start: 0.8386 (m) cc_final: 0.7990 (m) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.2377 time to fit residues: 76.5467 Evaluate side-chains 159 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 88 ASN B 230 ASN R 12 ASN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN H 179 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8937 Z= 0.257 Angle : 0.537 8.533 12119 Z= 0.283 Chirality : 0.043 0.182 1404 Planarity : 0.004 0.049 1507 Dihedral : 4.125 38.324 1220 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.88 % Allowed : 12.05 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1109 helix: 1.26 (0.26), residues: 407 sheet: -0.45 (0.30), residues: 266 loop : -0.41 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.034 0.002 PHE R 147 TYR 0.009 0.001 TYR B 105 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 0.987 Fit side-chains REVERT: B 234 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8997 (m-80) REVERT: B 243 THR cc_start: 0.8095 (p) cc_final: 0.7825 (p) REVERT: R 244 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7493 (mp) REVERT: R 277 MET cc_start: 0.8131 (tpp) cc_final: 0.7922 (mmt) REVERT: R 288 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7903 (tttp) REVERT: C 42 GLU cc_start: 0.8231 (pp20) cc_final: 0.7976 (pp20) REVERT: H 87 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6823 (mtm180) REVERT: A 251 ASP cc_start: 0.8975 (t70) cc_final: 0.8504 (t0) REVERT: A 305 CYS cc_start: 0.8285 (m) cc_final: 0.7973 (m) outliers start: 27 outliers final: 17 residues processed: 172 average time/residue: 0.2173 time to fit residues: 51.0535 Evaluate side-chains 148 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 266 HIS ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 HIS R 167 GLN H 39 GLN H 179 GLN A 244 HIS A 255 ASN A 311 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8937 Z= 0.428 Angle : 0.618 8.500 12119 Z= 0.326 Chirality : 0.046 0.191 1404 Planarity : 0.005 0.055 1507 Dihedral : 4.781 38.954 1219 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.16 % Allowed : 15.88 % Favored : 79.96 % 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: 0.23 (0.25), residues: 1109 helix: 1.21 (0.26), residues: 407 sheet: -0.23 (0.30), residues: 274 loop : -0.50 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 185 HIS 0.006 0.002 HIS B 183 PHE 0.035 0.002 PHE R 147 TYR 0.017 0.002 TYR B 105 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 0.966 Fit side-chains REVERT: B 234 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8988 (m-80) REVERT: B 261 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8449 (mt) REVERT: R 99 MET cc_start: 0.8458 (mmm) cc_final: 0.8206 (mmm) REVERT: R 172 MET cc_start: 0.7634 (tpp) cc_final: 0.6971 (tpp) REVERT: R 238 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7531 (mp) REVERT: R 270 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7211 (mp) REVERT: R 288 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7859 (tttp) REVERT: H 87 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7284 (mtm180) REVERT: A 20 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: A 32 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7224 (ttm-80) REVERT: A 305 CYS cc_start: 0.8385 (m) cc_final: 0.8077 (m) outliers start: 39 outliers final: 22 residues processed: 169 average time/residue: 0.2111 time to fit residues: 48.8853 Evaluate side-chains 152 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS A 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8937 Z= 0.151 Angle : 0.476 6.347 12119 Z= 0.252 Chirality : 0.040 0.143 1404 Planarity : 0.004 0.047 1507 Dihedral : 4.210 38.649 1219 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 19.08 % Favored : 78.57 % 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: 0.64 (0.25), residues: 1109 helix: 1.76 (0.26), residues: 404 sheet: -0.03 (0.30), residues: 264 loop : -0.46 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 PHE 0.033 0.001 PHE R 147 TYR 0.016 0.001 TYR B 59 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: B 261 LEU cc_start: 0.8675 (mm) cc_final: 0.8411 (mt) REVERT: R 56 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7369 (mp) REVERT: R 99 MET cc_start: 0.8458 (mmm) cc_final: 0.8236 (mmm) REVERT: R 179 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: R 238 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7484 (mp) REVERT: R 288 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7928 (tttp) REVERT: H 38 ARG cc_start: 0.9222 (ptt-90) cc_final: 0.8977 (ptp90) REVERT: H 87 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7125 (mtm180) REVERT: A 20 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: A 305 CYS cc_start: 0.8277 (m) cc_final: 0.7993 (m) outliers start: 22 outliers final: 10 residues processed: 150 average time/residue: 0.2336 time to fit residues: 47.3247 Evaluate side-chains 142 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8937 Z= 0.180 Angle : 0.474 6.329 12119 Z= 0.252 Chirality : 0.041 0.149 1404 Planarity : 0.004 0.056 1507 Dihedral : 4.105 35.631 1219 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 19.51 % Favored : 77.93 % 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: 0.72 (0.25), residues: 1109 helix: 1.84 (0.26), residues: 407 sheet: -0.04 (0.30), residues: 266 loop : -0.41 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 185 HIS 0.003 0.001 HIS B 91 PHE 0.033 0.001 PHE R 147 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.809 Fit side-chains REVERT: B 234 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: B 261 LEU cc_start: 0.8696 (mm) cc_final: 0.8437 (mt) REVERT: R 56 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7364 (mp) REVERT: R 99 MET cc_start: 0.8500 (mmm) cc_final: 0.8266 (mmm) REVERT: R 172 MET cc_start: 0.7602 (tpp) cc_final: 0.7231 (tpp) REVERT: R 179 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: R 238 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7341 (mp) REVERT: R 288 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7945 (tttp) REVERT: H 38 ARG cc_start: 0.9208 (ptt-90) cc_final: 0.9004 (ptp90) REVERT: H 87 ARG cc_start: 0.7421 (mtm110) cc_final: 0.7212 (mtm180) REVERT: A 20 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 305 CYS cc_start: 0.8275 (m) cc_final: 0.7983 (m) REVERT: A 327 THR cc_start: 0.7032 (OUTLIER) cc_final: 0.6823 (p) outliers start: 24 outliers final: 12 residues processed: 150 average time/residue: 0.2282 time to fit residues: 46.4074 Evaluate side-chains 145 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8937 Z= 0.164 Angle : 0.470 7.646 12119 Z= 0.248 Chirality : 0.040 0.144 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.027 34.624 1219 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.88 % Allowed : 19.51 % Favored : 77.61 % 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: 0.78 (0.26), residues: 1109 helix: 1.91 (0.27), residues: 408 sheet: -0.01 (0.30), residues: 266 loop : -0.41 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 185 HIS 0.002 0.001 HIS B 91 PHE 0.013 0.001 PHE A 189 TYR 0.017 0.001 TYR B 59 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.931 Fit side-chains REVERT: B 261 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8447 (mt) REVERT: R 56 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7328 (mp) REVERT: R 99 MET cc_start: 0.8488 (mmm) cc_final: 0.8258 (mmm) REVERT: R 172 MET cc_start: 0.7578 (tpp) cc_final: 0.7215 (tpp) REVERT: R 179 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7221 (m-10) REVERT: R 238 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7323 (mp) REVERT: R 288 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7973 (tttp) REVERT: H 87 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7131 (mtm180) REVERT: A 20 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: A 305 CYS cc_start: 0.8245 (m) cc_final: 0.7950 (m) outliers start: 27 outliers final: 16 residues processed: 153 average time/residue: 0.2426 time to fit residues: 50.0032 Evaluate side-chains 147 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8937 Z= 0.142 Angle : 0.465 7.650 12119 Z= 0.244 Chirality : 0.040 0.137 1404 Planarity : 0.004 0.055 1507 Dihedral : 3.881 32.258 1219 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.77 % Allowed : 19.83 % Favored : 77.40 % 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: 0.91 (0.26), residues: 1109 helix: 1.99 (0.27), residues: 409 sheet: 0.09 (0.31), residues: 266 loop : -0.33 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 185 HIS 0.002 0.001 HIS B 142 PHE 0.040 0.001 PHE R 147 TYR 0.009 0.001 TYR H 190 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.980 Fit side-chains REVERT: B 8 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6991 (mtm110) REVERT: B 234 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.9073 (m-80) REVERT: B 261 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8460 (mt) REVERT: R 56 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7380 (mp) REVERT: R 99 MET cc_start: 0.8539 (mmm) cc_final: 0.8323 (mmm) REVERT: R 147 PHE cc_start: 0.5317 (p90) cc_final: 0.4999 (m-80) REVERT: R 172 MET cc_start: 0.7536 (tpp) cc_final: 0.7190 (tpp) REVERT: R 238 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7398 (mp) REVERT: R 288 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7963 (tttp) REVERT: H 87 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7161 (mtm180) REVERT: A 20 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: A 305 CYS cc_start: 0.8213 (m) cc_final: 0.7938 (m) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 0.2266 time to fit residues: 44.5468 Evaluate side-chains 138 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8937 Z= 0.210 Angle : 0.495 9.103 12119 Z= 0.260 Chirality : 0.042 0.220 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.053 33.404 1219 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.56 % Allowed : 20.26 % Favored : 77.19 % 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: 0.90 (0.26), residues: 1109 helix: 1.96 (0.27), residues: 408 sheet: 0.11 (0.31), residues: 266 loop : -0.33 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 185 HIS 0.003 0.001 HIS B 91 PHE 0.030 0.001 PHE R 147 TYR 0.012 0.001 TYR H 235 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.982 Fit side-chains REVERT: B 8 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7048 (mtm110) REVERT: B 234 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9019 (m-80) REVERT: B 261 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (mt) REVERT: R 32 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8207 (tt) REVERT: R 56 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7382 (mp) REVERT: R 99 MET cc_start: 0.8489 (mmm) cc_final: 0.8249 (mmm) REVERT: R 172 MET cc_start: 0.7566 (tpp) cc_final: 0.7206 (tpp) REVERT: R 238 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7371 (mp) REVERT: R 288 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7972 (tttp) REVERT: A 20 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: A 305 CYS cc_start: 0.8257 (m) cc_final: 0.7975 (m) outliers start: 24 outliers final: 13 residues processed: 139 average time/residue: 0.2225 time to fit residues: 42.1021 Evaluate side-chains 136 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8937 Z= 0.170 Angle : 0.486 10.659 12119 Z= 0.254 Chirality : 0.041 0.246 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.012 33.363 1219 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 20.58 % Favored : 76.87 % 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: 0.94 (0.26), residues: 1109 helix: 1.96 (0.27), residues: 414 sheet: 0.14 (0.31), residues: 266 loop : -0.30 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP R 185 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE A 189 TYR 0.010 0.001 TYR H 235 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.919 Fit side-chains REVERT: B 8 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7057 (mtm110) REVERT: B 217 MET cc_start: 0.7522 (mmt) cc_final: 0.7272 (mmm) REVERT: B 234 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9067 (m-80) REVERT: B 261 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8493 (mt) REVERT: R 32 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8205 (tt) REVERT: R 56 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7366 (mp) REVERT: R 99 MET cc_start: 0.8482 (mmm) cc_final: 0.8245 (mmm) REVERT: R 172 MET cc_start: 0.7566 (tpp) cc_final: 0.7242 (tpp) REVERT: R 238 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7366 (mp) REVERT: R 288 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7973 (tttp) REVERT: A 20 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7803 (m-30) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.2384 time to fit residues: 45.9955 Evaluate side-chains 141 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8937 Z= 0.154 Angle : 0.482 10.713 12119 Z= 0.253 Chirality : 0.041 0.256 1404 Planarity : 0.004 0.052 1507 Dihedral : 3.933 32.938 1219 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 20.26 % Favored : 77.29 % 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: 1.00 (0.26), residues: 1109 helix: 1.94 (0.27), residues: 415 sheet: 0.22 (0.31), residues: 266 loop : -0.24 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP R 185 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR B 59 ARG 0.010 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.747 Fit side-chains REVERT: B 8 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7063 (mtm110) REVERT: B 217 MET cc_start: 0.7499 (mmt) cc_final: 0.7247 (mmm) REVERT: B 234 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9036 (m-80) REVERT: B 261 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (mt) REVERT: R 56 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7367 (mp) REVERT: R 99 MET cc_start: 0.8479 (mmm) cc_final: 0.8269 (mmm) REVERT: R 172 MET cc_start: 0.7539 (tpp) cc_final: 0.7222 (tpp) REVERT: R 238 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7394 (mp) REVERT: R 288 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7973 (tttp) REVERT: A 20 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7789 (m-30) outliers start: 23 outliers final: 16 residues processed: 139 average time/residue: 0.2327 time to fit residues: 43.3791 Evaluate side-chains 138 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109726 restraints weight = 9740.568| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.25 r_work: 0.3072 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.219 Angle : 0.510 10.795 12119 Z= 0.267 Chirality : 0.042 0.266 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.089 34.484 1219 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 21.00 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1109 helix: 1.90 (0.27), residues: 414 sheet: 0.20 (0.31), residues: 266 loop : -0.27 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 185 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR H 235 ARG 0.010 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.21 seconds wall clock time: 41 minutes 5.65 seconds (2465.65 seconds total)