Starting phenix.real_space_refine on Tue Jun 25 21:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_2024/8x17_37986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_2024/8x17_37986.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_2024/8x17_37986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_2024/8x17_37986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_2024/8x17_37986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/06_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 5.21, per 1000 atoms: 0.60 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: 3.44 Conformation dependent library (CDL) restraints added in 1.6 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: 1.73 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: 2.74 Time building geometry restraints manager: 3.71 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=" C06 XS0 R 401 " pdb=" C07 XS0 R 401 " ideal model delta sigma weight residual 1.533 1.289 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C16 XS0 R 401 " pdb="CL19 XS0 R 401 " ideal model delta sigma weight residual 1.737 1.889 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C03 XS0 R 401 " pdb=" N02 XS0 R 401 " ideal model delta sigma weight residual 1.334 1.471 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C05 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 1.411 1.527 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " ideal model delta sigma weight residual 1.529 1.640 -0.111 2.00e-02 2.50e+03 3.09e+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=" 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=" N10 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 109.29 95.97 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" N10 XS0 R 401 " ideal model delta sigma weight residual 112.51 124.11 -11.60 3.00e+00 1.11e-01 1.50e+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: 4865 17.35 - 34.71: 335 34.71 - 52.06: 69 52.06 - 69.41: 11 69.41 - 86.76: 5 Dihedral angle restraints: 5285 sinusoidal: 2009 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 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1333 0.093 - 0.186: 68 0.186 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 3 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 2.57 3.04 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" C07 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O29 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.75 2.29 0.45 2.00e-01 2.50e+01 5.11e+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 2.59 2.21 0.38 2.00e-01 2.50e+01 3.61e+00 ... (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: 1.040 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: 3.800 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.560 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- 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 : 0.005 0.244 8937 Z= 0.280 Angle : 0.555 13.321 12119 Z= 0.321 Chirality : 0.043 0.466 1404 Planarity : 0.003 0.047 1507 Dihedral : 12.618 86.763 3168 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 : 0.987 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: 0.2191 time to fit residues: 70.3809 Evaluate side-chains 159 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8937 Z= 0.259 Angle : 0.539 8.756 12119 Z= 0.283 Chirality : 0.044 0.173 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.769 56.139 1241 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.99 % Allowed : 12.05 % Favored : 84.97 % 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 (0.25), residues: 1109 helix: 1.24 (0.26), residues: 407 sheet: -0.41 (0.30), residues: 265 loop : -0.42 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.035 0.002 PHE R 147 TYR 0.009 0.001 TYR B 105 ARG 0.005 0.001 ARG B 219 *********************** 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 180 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.036 Fit side-chains REVERT: B 234 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9000 (m-80) REVERT: B 243 THR cc_start: 0.8112 (p) cc_final: 0.7848 (p) REVERT: R 244 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7476 (mp) REVERT: R 288 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7906 (tttp) REVERT: C 42 GLU cc_start: 0.8235 (pp20) cc_final: 0.7980 (pp20) REVERT: H 87 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6837 (mtm180) REVERT: A 251 ASP cc_start: 0.8984 (t70) cc_final: 0.8513 (t0) REVERT: A 305 CYS cc_start: 0.8283 (m) cc_final: 0.7972 (m) outliers start: 28 outliers final: 17 residues processed: 175 average time/residue: 0.2135 time to fit residues: 51.1871 Evaluate side-chains 151 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.0370 chunk 100 optimal weight: 3.9990 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: 9.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8937 Z= 0.320 Angle : 0.548 6.951 12119 Z= 0.291 Chirality : 0.044 0.164 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.895 52.066 1240 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.09 % Allowed : 15.78 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1109 helix: 1.43 (0.26), residues: 407 sheet: -0.31 (0.29), residues: 277 loop : -0.36 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 185 HIS 0.005 0.001 HIS B 91 PHE 0.035 0.002 PHE R 147 TYR 0.012 0.002 TYR B 105 ARG 0.006 0.001 ARG A 313 *********************** 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 168 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.990 Fit side-chains REVERT: B 234 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8984 (m-80) REVERT: B 261 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 312 ASP cc_start: 0.8078 (p0) cc_final: 0.7823 (p0) REVERT: R 172 MET cc_start: 0.7604 (tpp) cc_final: 0.6896 (tpp) REVERT: R 238 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7595 (mp) REVERT: R 244 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7535 (mp) REVERT: R 288 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7894 (tttp) REVERT: H 87 ARG cc_start: 0.7321 (mtm110) cc_final: 0.7059 (mtm180) REVERT: A 20 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 305 CYS cc_start: 0.8334 (m) cc_final: 0.8045 (m) outliers start: 29 outliers final: 16 residues processed: 161 average time/residue: 0.2122 time to fit residues: 46.6320 Evaluate side-chains 148 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 27 ILE Chi-restraints excluded: chain R residue 32 LEU 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 238 LEU 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 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: 0.7980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 266 HIS ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 244 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8937 Z= 0.167 Angle : 0.479 6.073 12119 Z= 0.253 Chirality : 0.040 0.140 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.607 53.341 1240 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.77 % Allowed : 17.91 % Favored : 79.32 % 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: 0.71 (0.25), residues: 1109 helix: 1.83 (0.26), residues: 405 sheet: -0.07 (0.30), residues: 266 loop : -0.39 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 185 HIS 0.003 0.001 HIS B 91 PHE 0.034 0.001 PHE R 147 TYR 0.010 0.001 TYR H 235 ARG 0.006 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 155 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.9024 (m-80) REVERT: B 261 LEU cc_start: 0.8657 (mm) cc_final: 0.8363 (mt) REVERT: R 56 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7344 (mp) REVERT: R 238 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (mp) REVERT: R 288 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7935 (tttp) REVERT: H 38 ARG cc_start: 0.9217 (ptt-90) cc_final: 0.8962 (ptp90) REVERT: H 87 ARG cc_start: 0.7345 (mtm110) cc_final: 0.7048 (mtm180) REVERT: A 20 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: A 305 CYS cc_start: 0.8269 (m) cc_final: 0.7971 (m) outliers start: 26 outliers final: 14 residues processed: 149 average time/residue: 0.2105 time to fit residues: 42.9412 Evaluate side-chains 143 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 230 ASN Chi-restraints excluded: chain B residue 234 PHE 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 46 THR Chi-restraints excluded: chain R residue 56 LEU 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 63 THR 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: 5.9990 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** H 39 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8937 Z= 0.246 Angle : 0.500 7.118 12119 Z= 0.264 Chirality : 0.042 0.157 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.636 52.405 1240 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.09 % Allowed : 18.55 % Favored : 78.36 % 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: 0.68 (0.25), residues: 1109 helix: 1.81 (0.26), residues: 404 sheet: -0.02 (0.30), residues: 264 loop : -0.46 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 185 HIS 0.004 0.001 HIS B 91 PHE 0.034 0.001 PHE R 147 TYR 0.011 0.001 TYR H 235 ARG 0.007 0.001 ARG A 313 *********************** 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 158 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: B 261 LEU cc_start: 0.8702 (mm) cc_final: 0.8442 (mt) REVERT: R 56 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7375 (mp) REVERT: R 172 MET cc_start: 0.7618 (tpp) cc_final: 0.7188 (tpp) REVERT: R 238 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7478 (mp) REVERT: R 288 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7950 (tttp) REVERT: H 38 ARG cc_start: 0.9218 (ptt-90) cc_final: 0.8991 (ptp90) REVERT: H 87 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7233 (mtm180) REVERT: A 20 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 305 CYS cc_start: 0.8301 (m) cc_final: 0.8021 (m) REVERT: A 327 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6700 (p) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 0.2251 time to fit residues: 46.0832 Evaluate side-chains 147 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 266 HIS 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 46 THR Chi-restraints excluded: chain R residue 56 LEU 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 238 LEU Chi-restraints excluded: chain R residue 262 LEU 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 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE 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: 0.8980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8937 Z= 0.166 Angle : 0.475 6.525 12119 Z= 0.250 Chirality : 0.040 0.146 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.517 52.572 1240 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.99 % Allowed : 19.51 % Favored : 77.51 % 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: 0.79 (0.26), residues: 1109 helix: 1.90 (0.26), residues: 408 sheet: -0.00 (0.30), residues: 266 loop : -0.39 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 185 HIS 0.004 0.001 HIS B 266 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR H 235 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 156 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.030 Fit side-chains REVERT: B 8 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6989 (mtm110) REVERT: B 234 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: B 261 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8453 (mt) REVERT: R 56 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7352 (mp) REVERT: R 172 MET cc_start: 0.7595 (tpp) cc_final: 0.7231 (tpp) REVERT: R 238 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7426 (mp) REVERT: R 288 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7953 (tttp) REVERT: H 87 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7238 (mtm180) REVERT: A 20 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 305 CYS cc_start: 0.8249 (m) cc_final: 0.7969 (m) outliers start: 28 outliers final: 16 residues processed: 150 average time/residue: 0.2134 time to fit residues: 43.4271 Evaluate side-chains 145 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 46 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 191 VAL 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 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 20 ASP 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: 0.8980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 0.0370 chunk 42 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8937 Z= 0.155 Angle : 0.475 8.239 12119 Z= 0.249 Chirality : 0.040 0.152 1404 Planarity : 0.004 0.054 1507 Dihedral : 4.443 52.238 1240 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.77 % Allowed : 19.94 % 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: 0.88 (0.26), residues: 1109 helix: 1.97 (0.27), residues: 408 sheet: 0.08 (0.31), residues: 266 loop : -0.35 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 185 HIS 0.002 0.001 HIS B 91 PHE 0.039 0.001 PHE R 147 TYR 0.010 0.001 TYR B 59 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 148 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.987 Fit side-chains REVERT: B 8 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6980 (mtm110) REVERT: B 261 LEU cc_start: 0.8720 (mm) cc_final: 0.8467 (mt) REVERT: R 56 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7361 (mp) REVERT: R 147 PHE cc_start: 0.5395 (p90) cc_final: 0.5012 (m-80) REVERT: R 172 MET cc_start: 0.7541 (tpp) cc_final: 0.7202 (tpp) REVERT: R 179 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: R 238 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7433 (mp) REVERT: R 288 LYS cc_start: 0.8213 (ttpt) cc_final: 0.8009 (tttp) REVERT: H 87 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7133 (mtm180) REVERT: A 20 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 305 CYS cc_start: 0.8224 (m) cc_final: 0.7938 (m) outliers start: 26 outliers final: 17 residues processed: 144 average time/residue: 0.2274 time to fit residues: 44.2336 Evaluate side-chains 139 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS 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 46 THR 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 H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 THR 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 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: 0.5980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8937 Z= 0.152 Angle : 0.474 9.102 12119 Z= 0.247 Chirality : 0.040 0.183 1404 Planarity : 0.004 0.051 1507 Dihedral : 4.347 51.436 1240 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.67 % Allowed : 20.47 % 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: 0.97 (0.26), residues: 1109 helix: 2.01 (0.27), residues: 409 sheet: 0.17 (0.31), residues: 266 loop : -0.30 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 185 HIS 0.002 0.001 HIS R 79 PHE 0.031 0.001 PHE R 147 TYR 0.009 0.001 TYR H 190 ARG 0.010 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 146 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.991 Fit side-chains REVERT: B 8 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6993 (mtm110) REVERT: B 261 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8485 (mt) REVERT: R 56 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7403 (mp) REVERT: R 172 MET cc_start: 0.7571 (tpp) cc_final: 0.7215 (tpp) REVERT: R 179 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: R 238 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7329 (mp) REVERT: H 87 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7142 (mtm180) REVERT: A 20 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: A 305 CYS cc_start: 0.8222 (m) cc_final: 0.7943 (m) outliers start: 25 outliers final: 15 residues processed: 141 average time/residue: 0.2157 time to fit residues: 41.4886 Evaluate side-chains 136 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 46 THR 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 H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 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 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8937 Z= 0.141 Angle : 0.475 9.807 12119 Z= 0.247 Chirality : 0.040 0.230 1404 Planarity : 0.004 0.054 1507 Dihedral : 4.242 51.556 1240 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.24 % Allowed : 21.54 % Favored : 76.23 % 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: 1.08 (0.26), residues: 1109 helix: 2.09 (0.27), residues: 408 sheet: 0.25 (0.31), residues: 266 loop : -0.24 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 185 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR H 190 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 144 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.914 Fit side-chains REVERT: B 8 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7000 (mtm110) REVERT: B 234 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9049 (m-80) REVERT: B 261 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8491 (mt) REVERT: R 32 LEU cc_start: 0.8209 (tt) cc_final: 0.7886 (tt) REVERT: R 56 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7375 (mp) REVERT: R 172 MET cc_start: 0.7539 (tpp) cc_final: 0.7229 (tpp) REVERT: R 238 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7342 (mp) REVERT: H 87 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7170 (mtm180) outliers start: 21 outliers final: 14 residues processed: 142 average time/residue: 0.2146 time to fit residues: 41.3533 Evaluate side-chains 136 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 159 THR 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 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 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL 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: 0.0980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8937 Z= 0.151 Angle : 0.480 10.939 12119 Z= 0.250 Chirality : 0.041 0.263 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.234 49.985 1240 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.13 % Allowed : 21.54 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1109 helix: 2.04 (0.27), residues: 414 sheet: 0.31 (0.31), residues: 273 loop : -0.25 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP R 185 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR H 190 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 135 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.089 Fit side-chains REVERT: B 8 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7015 (mtm110) REVERT: B 228 ASP cc_start: 0.8385 (p0) cc_final: 0.7933 (p0) REVERT: B 234 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9041 (m-80) REVERT: B 261 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (mt) REVERT: R 32 LEU cc_start: 0.8186 (tt) cc_final: 0.7800 (tt) REVERT: R 56 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7378 (mp) REVERT: R 172 MET cc_start: 0.7513 (tpp) cc_final: 0.7190 (tpp) REVERT: R 238 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 277 MET cc_start: 0.7071 (mmt) cc_final: 0.6854 (mmt) REVERT: H 87 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7259 (mtm180) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 0.2193 time to fit residues: 40.1735 Evaluate side-chains 134 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL 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: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109639 restraints weight = 8618.398| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.19 r_work: 0.2998 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8937 Z= 0.357 Angle : 0.574 11.093 12119 Z= 0.301 Chirality : 0.045 0.265 1404 Planarity : 0.004 0.057 1507 Dihedral : 4.778 47.140 1240 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.35 % Allowed : 21.32 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.76 (0.26), residues: 1109 helix: 1.75 (0.26), residues: 411 sheet: 0.17 (0.31), residues: 264 loop : -0.42 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 185 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE R 48 TYR 0.021 0.002 TYR B 59 ARG 0.010 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.13 seconds wall clock time: 39 minutes 48.92 seconds (2388.92 seconds total)