Starting phenix.real_space_refine on Sat Dec 9 00:58:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa3_33086/12_2023/7xa3_33086.pdb" } resolution = 2.9 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6116 2.51 5 N 1628 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 196": "NH1" <-> "NH2" Residue "R ARG 206": "NH1" <-> "NH2" Residue "R ARG 231": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R ARG 313": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9591 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2377 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain: "L" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1841 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 7.12, per 1000 atoms: 0.74 Number of scatterers: 9591 At special positions: 0 Unit cell: (110.526, 140.946, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1777 8.00 N 1628 7.00 C 6116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 32 " - pdb=" SG CYS R 277 " distance=2.02 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.9 seconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 39.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'R' and resid 34 through 70 removed outlier: 3.993A pdb=" N LYS R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) Proline residue: R 46 - end of helix Processing helix chain 'R' and resid 75 through 94 removed outlier: 4.645A pdb=" N THR R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 102 Processing helix chain 'R' and resid 109 through 144 removed outlier: 3.592A pdb=" N GLY R 118 " --> pdb=" O LYS R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 152 removed outlier: 3.660A pdb=" N LYS R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 178 Proline residue: R 174 - end of helix removed outlier: 3.638A pdb=" N PHE R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 211 removed outlier: 3.564A pdb=" N THR R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 204 " --> pdb=" O ASN R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 232 removed outlier: 3.711A pdb=" N GLY R 224 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 269 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 276 through 306 removed outlier: 3.960A pdb=" N SER R 281 " --> pdb=" O CYS R 277 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 298 " --> pdb=" O GLY R 294 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 323 Processing helix chain 'L' and resid 57 through 69 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.881A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.123A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.783A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.927A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.290A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.657A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.636A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.549A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.650A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 179 through 184 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.641A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.511A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.902A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.024A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.642A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.642A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.516A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.768A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.193A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.862A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR E 190 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.862A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1416 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: 2.90 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3040 1.34 - 1.46: 2065 1.46 - 1.58: 4589 1.58 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 9793 Sorted by residual: bond pdb=" C ALA R 30 " pdb=" N PRO R 31 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.31e+00 bond pdb=" C VAL R 173 " pdb=" N PRO R 174 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" C PRO R 46 " pdb=" N PRO R 47 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.18e+00 bond pdb=" C THR R 257 " pdb=" N PRO R 258 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.21e+00 bond pdb=" CA ASP B 210 " pdb=" C ASP B 210 " ideal model delta sigma weight residual 1.518 1.586 -0.069 4.01e-02 6.22e+02 2.92e+00 ... (remaining 9788 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.31: 108 104.31 - 111.75: 4440 111.75 - 119.19: 3489 119.19 - 126.64: 5079 126.64 - 134.08: 139 Bond angle restraints: 13255 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" N ALA R 30 " pdb=" CA ALA R 30 " pdb=" C ALA R 30 " ideal model delta sigma weight residual 109.81 119.48 -9.67 2.21e+00 2.05e-01 1.92e+01 angle pdb=" N PRO R 46 " pdb=" CA PRO R 46 " pdb=" C PRO R 46 " ideal model delta sigma weight residual 110.70 115.36 -4.66 1.22e+00 6.72e-01 1.46e+01 angle pdb=" CA PRO R 46 " pdb=" C PRO R 46 " pdb=" N PRO R 47 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" N LEU R 45 " pdb=" CA LEU R 45 " pdb=" C LEU R 45 " ideal model delta sigma weight residual 109.81 117.73 -7.92 2.21e+00 2.05e-01 1.28e+01 ... (remaining 13250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 5633 15.46 - 30.92: 165 30.92 - 46.38: 28 46.38 - 61.84: 0 61.84 - 77.30: 1 Dihedral angle restraints: 5827 sinusoidal: 2290 harmonic: 3537 Sorted by residual: dihedral pdb=" CB CYS L 11 " pdb=" SG CYS L 11 " pdb=" SG CYS L 36 " pdb=" CB CYS L 36 " ideal model delta sinusoidal sigma weight residual -86.00 -163.30 77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS L 12 " pdb=" SG CYS L 12 " pdb=" SG CYS L 52 " pdb=" CB CYS L 52 " ideal model delta sinusoidal sigma weight residual 93.00 128.18 -35.18 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA GLN E 142 " pdb=" C GLN E 142 " pdb=" N ALA E 143 " pdb=" CA ALA E 143 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1034 0.048 - 0.095: 354 0.095 - 0.143: 86 0.143 - 0.190: 24 0.190 - 0.238: 5 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB VAL L 47 " pdb=" CA VAL L 47 " pdb=" CG1 VAL L 47 " pdb=" CG2 VAL L 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LEU R 95 " pdb=" N LEU R 95 " pdb=" C LEU R 95 " pdb=" CB LEU R 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO R 31 " pdb=" N PRO R 31 " pdb=" C PRO R 31 " pdb=" CB PRO R 31 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1500 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 303 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C ILE R 303 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE R 303 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE R 304 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " -0.018 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP E 110 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 241 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.032 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1664 2.78 - 3.31: 8568 3.31 - 3.84: 15270 3.84 - 4.37: 17497 4.37 - 4.90: 31486 Nonbonded interactions: 74485 Sorted by model distance: nonbonded pdb=" O GLY R 175 " pdb=" OG1 THR R 179 " model vdw 2.250 2.440 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.291 2.440 nonbonded pdb=" OG SER B 166 " pdb=" OD1 ASP B 168 " model vdw 2.301 2.440 nonbonded pdb=" OG SER E 6 " pdb=" OG SER E 20 " model vdw 2.321 2.440 nonbonded pdb=" O GLY E 111 " pdb=" OG SER E 184 " model vdw 2.340 2.440 ... (remaining 74480 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: 1.730 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: 0.000 Extract box with map and model: 1.840 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 0.071 9793 Z= 0.304 Angle : 0.850 10.720 13255 Z= 0.486 Chirality : 0.052 0.238 1503 Planarity : 0.006 0.057 1674 Dihedral : 7.874 45.992 3530 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1204 helix: 1.43 (0.21), residues: 428 sheet: 0.96 (0.29), residues: 286 loop : -0.86 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP E 110 HIS 0.009 0.002 HIS B 230 PHE 0.032 0.003 PHE A 354 TYR 0.031 0.003 TYR E 93 ARG 0.012 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 1.0877 time to fit residues: 331.4102 Evaluate side-chains 233 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN R 110 ASN R 121 HIS R 260 ASN R 285 GLN R 288 GLN A 188 HIS A 204 GLN A 269 ASN A 304 GLN A 346 ASN B 96 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN B 271 HIS B 273 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9793 Z= 0.171 Angle : 0.537 6.988 13255 Z= 0.285 Chirality : 0.042 0.311 1503 Planarity : 0.004 0.042 1674 Dihedral : 4.171 17.303 1316 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.76 % Allowed : 11.50 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.45 (0.23), residues: 1204 helix: 2.45 (0.24), residues: 431 sheet: 1.30 (0.29), residues: 282 loop : -0.62 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 344 HIS 0.008 0.001 HIS A 188 PHE 0.024 0.002 PHE R 53 TYR 0.019 0.002 TYR R 124 ARG 0.006 0.000 ARG R 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 259 average time/residue: 1.1265 time to fit residues: 313.1222 Evaluate side-chains 264 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 11 average time/residue: 0.2788 time to fit residues: 5.4187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN R 288 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 346 ASN B 264 GLN B 345 ASN E 232 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9793 Z= 0.291 Angle : 0.590 8.365 13255 Z= 0.313 Chirality : 0.045 0.386 1503 Planarity : 0.004 0.040 1674 Dihedral : 4.385 17.290 1316 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.61 % Allowed : 14.73 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.43 (0.23), residues: 1204 helix: 2.41 (0.24), residues: 425 sheet: 1.11 (0.29), residues: 294 loop : -0.49 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 174 HIS 0.008 0.002 HIS B 67 PHE 0.022 0.002 PHE R 156 TYR 0.024 0.002 TYR R 120 ARG 0.009 0.001 ARG R 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 261 average time/residue: 1.1281 time to fit residues: 316.8209 Evaluate side-chains 256 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 9 residues processed: 13 average time/residue: 0.2353 time to fit residues: 5.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 271 HIS B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9793 Z= 0.181 Angle : 0.520 9.661 13255 Z= 0.273 Chirality : 0.042 0.366 1503 Planarity : 0.003 0.040 1674 Dihedral : 4.132 15.867 1316 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.80 % Allowed : 16.25 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.58 (0.24), residues: 1204 helix: 2.67 (0.25), residues: 425 sheet: 1.09 (0.29), residues: 292 loop : -0.46 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.023 0.001 PHE R 156 TYR 0.013 0.002 TYR R 120 ARG 0.004 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 1.111 Fit side-chains outliers start: 40 outliers final: 25 residues processed: 243 average time/residue: 1.0929 time to fit residues: 285.9814 Evaluate side-chains 241 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 15 average time/residue: 0.4001 time to fit residues: 8.7410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN A 346 ASN B 271 HIS B 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9793 Z= 0.205 Angle : 0.548 11.597 13255 Z= 0.282 Chirality : 0.043 0.348 1503 Planarity : 0.003 0.040 1674 Dihedral : 4.139 15.929 1316 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.80 % Allowed : 17.21 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.53 (0.24), residues: 1204 helix: 2.67 (0.25), residues: 425 sheet: 1.04 (0.29), residues: 288 loop : -0.51 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 216 HIS 0.004 0.001 HIS B 67 PHE 0.027 0.002 PHE R 53 TYR 0.015 0.001 TYR R 120 ARG 0.005 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.149 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 231 average time/residue: 1.1641 time to fit residues: 290.0850 Evaluate side-chains 242 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 13 average time/residue: 0.3669 time to fit residues: 7.3336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 161 GLN B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9793 Z= 0.172 Angle : 0.528 11.156 13255 Z= 0.271 Chirality : 0.042 0.354 1503 Planarity : 0.003 0.039 1674 Dihedral : 4.010 18.304 1316 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.42 % Allowed : 17.87 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.60 (0.24), residues: 1204 helix: 2.76 (0.25), residues: 425 sheet: 1.01 (0.28), residues: 291 loop : -0.46 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.029 0.002 PHE R 53 TYR 0.012 0.001 TYR R 120 ARG 0.004 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 246 average time/residue: 1.3281 time to fit residues: 357.7002 Evaluate side-chains 244 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 14 average time/residue: 0.3933 time to fit residues: 8.4371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 0.0010 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 161 GLN B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9793 Z= 0.143 Angle : 0.517 10.374 13255 Z= 0.264 Chirality : 0.041 0.336 1503 Planarity : 0.003 0.039 1674 Dihedral : 3.863 18.211 1316 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.33 % Allowed : 18.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.68 (0.24), residues: 1204 helix: 2.83 (0.25), residues: 424 sheet: 0.98 (0.28), residues: 296 loop : -0.37 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 216 HIS 0.002 0.001 HIS E 34 PHE 0.029 0.001 PHE R 53 TYR 0.016 0.001 TYR R 124 ARG 0.006 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 242 average time/residue: 1.0651 time to fit residues: 278.2719 Evaluate side-chains 236 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 7 average time/residue: 0.2749 time to fit residues: 3.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 161 GLN B 345 ASN E 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9793 Z= 0.160 Angle : 0.521 10.285 13255 Z= 0.267 Chirality : 0.041 0.302 1503 Planarity : 0.003 0.038 1674 Dihedral : 3.872 19.309 1316 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.95 % Allowed : 18.82 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.72 (0.24), residues: 1204 helix: 2.90 (0.25), residues: 424 sheet: 0.97 (0.28), residues: 296 loop : -0.35 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.029 0.001 PHE R 156 TYR 0.009 0.001 TYR R 120 ARG 0.006 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 241 average time/residue: 1.0752 time to fit residues: 279.9268 Evaluate side-chains 240 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 8 average time/residue: 0.2344 time to fit residues: 4.4801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 161 GLN B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9793 Z= 0.293 Angle : 0.606 10.885 13255 Z= 0.314 Chirality : 0.044 0.312 1503 Planarity : 0.004 0.039 1674 Dihedral : 4.318 26.536 1316 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.76 % Allowed : 20.15 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1204 helix: 2.57 (0.25), residues: 426 sheet: 0.93 (0.28), residues: 303 loop : -0.40 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 87 HIS 0.005 0.001 HIS B 67 PHE 0.028 0.002 PHE R 156 TYR 0.021 0.002 TYR R 120 ARG 0.007 0.001 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 243 average time/residue: 1.0126 time to fit residues: 266.5189 Evaluate side-chains 239 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 8 average time/residue: 0.6024 time to fit residues: 6.9493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.0020 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 346 ASN B 37 GLN B 161 GLN B 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9793 Z= 0.169 Angle : 0.553 11.136 13255 Z= 0.282 Chirality : 0.042 0.292 1503 Planarity : 0.003 0.038 1674 Dihedral : 4.058 22.180 1316 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.62 % Allowed : 21.86 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.63 (0.24), residues: 1204 helix: 2.75 (0.25), residues: 423 sheet: 1.00 (0.28), residues: 296 loop : -0.38 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.030 0.002 PHE R 156 TYR 0.014 0.001 TYR R 124 ARG 0.006 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 236 average time/residue: 1.0402 time to fit residues: 265.5381 Evaluate side-chains 235 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 4 average time/residue: 0.3654 time to fit residues: 3.3061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.0010 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN B 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125010 restraints weight = 13952.573| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.93 r_work: 0.3515 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9793 Z= 0.168 Angle : 0.559 11.063 13255 Z= 0.286 Chirality : 0.042 0.324 1503 Planarity : 0.003 0.039 1674 Dihedral : 4.003 22.066 1316 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.19 % Allowed : 21.77 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.61 (0.24), residues: 1204 helix: 2.75 (0.25), residues: 420 sheet: 0.97 (0.28), residues: 295 loop : -0.37 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.029 0.002 PHE R 156 TYR 0.015 0.001 TYR R 80 ARG 0.006 0.000 ARG B 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4938.02 seconds wall clock time: 88 minutes 1.10 seconds (5281.10 seconds total)