Starting phenix.real_space_refine on Sat Aug 3 16:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/08_2024/8ykx_39375_neut.cif" } resolution = 2.69 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= 0.001 sd= 0.079 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 56 5.16 5 C 5576 2.51 5 N 1472 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 33": "OE1" <-> "OE2" Residue "R GLU 153": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2276 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1699 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2558 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1728 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 441 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'MAE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.62 Number of scatterers: 8710 At special positions: 0 Unit cell: (86.87, 119.72, 132.13, 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 56 16.00 O 1606 8.00 N 1472 7.00 C 5576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.61 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: 3.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 39.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'R' and resid 11 through 49 removed outlier: 4.065A pdb=" N ALA R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 75 through 86 removed outlier: 4.231A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 217 Processing helix chain 'R' and resid 227 through 259 removed outlier: 3.577A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.564A pdb=" N ARG R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 286 Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 286 through 297 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 309 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.649A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.971A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.026A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.582A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.790A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 8 through 25 removed outlier: 3.862A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.204A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.598A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.783A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.188A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.997A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.743A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.348A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1287 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: 2.92 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2190 1.33 - 1.45: 1820 1.45 - 1.58: 4796 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8888 Sorted by residual: bond pdb=" C LEU R 214 " pdb=" N LYS R 215 " ideal model delta sigma weight residual 1.335 1.431 -0.097 1.36e-02 5.41e+03 5.05e+01 bond pdb=" C PHE R 296 " pdb=" N LEU R 297 " ideal model delta sigma weight residual 1.334 1.410 -0.076 1.43e-02 4.89e+03 2.83e+01 bond pdb=" CA ARG R 281 " pdb=" C ARG R 281 " ideal model delta sigma weight residual 1.521 1.571 -0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C ARG R 281 " pdb=" N PRO R 282 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.28e-02 6.10e+03 1.36e+01 bond pdb=" N THR R 269 " pdb=" CA THR R 269 " ideal model delta sigma weight residual 1.458 1.411 0.047 1.90e-02 2.77e+03 6.15e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.88: 206 106.88 - 113.67: 4945 113.67 - 120.46: 3370 120.46 - 127.25: 3435 127.25 - 134.04: 91 Bond angle restraints: 12047 Sorted by residual: angle pdb=" N LEU R 231 " pdb=" CA LEU R 231 " pdb=" C LEU R 231 " ideal model delta sigma weight residual 111.28 105.84 5.44 1.09e+00 8.42e-01 2.50e+01 angle pdb=" N THR R 269 " pdb=" CA THR R 269 " pdb=" C THR R 269 " ideal model delta sigma weight residual 111.00 100.08 10.92 2.80e+00 1.28e-01 1.52e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.91 109.26 2.65 8.90e-01 1.26e+00 8.89e+00 angle pdb=" N ASP A 251 " pdb=" CA ASP A 251 " pdb=" C ASP A 251 " ideal model delta sigma weight residual 111.07 108.12 2.95 1.07e+00 8.73e-01 7.59e+00 ... (remaining 12042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4721 17.53 - 35.07: 400 35.07 - 52.60: 110 52.60 - 70.13: 17 70.13 - 87.66: 12 Dihedral angle restraints: 5260 sinusoidal: 2003 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 50.10 42.90 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ILE R 89 " pdb=" C ILE R 89 " pdb=" N TYR R 90 " pdb=" CA TYR R 90 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 951 0.035 - 0.070: 286 0.070 - 0.105: 101 0.105 - 0.140: 40 0.140 - 0.175: 4 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA LYS R 135 " pdb=" N LYS R 135 " pdb=" C LYS R 135 " pdb=" CB LYS R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA THR R 269 " pdb=" N THR R 269 " pdb=" C THR R 269 " pdb=" CB THR R 269 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR R 280 " pdb=" CA THR R 280 " pdb=" OG1 THR R 280 " pdb=" CG2 THR R 280 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1379 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 296 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C PHE R 296 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE R 296 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 297 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.166 9.50e-02 1.11e+02 7.47e-02 3.75e+00 pdb=" NE ARG B 134 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 280 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C THR R 280 " 0.031 2.00e-02 2.50e+03 pdb=" O THR R 280 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG R 281 " -0.011 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1408 2.76 - 3.29: 8515 3.29 - 3.83: 14726 3.83 - 4.36: 18273 4.36 - 4.90: 31851 Nonbonded interactions: 74773 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.305 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.312 3.040 nonbonded pdb=" O GLY R 37 " pdb=" ND2 ASN R 41 " model vdw 2.351 3.120 ... (remaining 74768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.120 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 8888 Z= 0.244 Angle : 0.609 10.915 12047 Z= 0.337 Chirality : 0.042 0.175 1382 Planarity : 0.004 0.075 1518 Dihedral : 14.755 87.663 3155 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.43 % Allowed : 13.73 % Favored : 85.84 % 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: 1.26 (0.26), residues: 1097 helix: 2.06 (0.27), residues: 388 sheet: 0.55 (0.31), residues: 277 loop : -0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS R 103 PHE 0.009 0.001 PHE R 205 TYR 0.013 0.001 TYR E 103 ARG 0.010 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 MET cc_start: 0.8417 (ttm) cc_final: 0.8195 (mtp) REVERT: R 281 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (ttm170) REVERT: A 29 LYS cc_start: 0.7862 (tttt) cc_final: 0.7484 (tmmt) REVERT: A 242 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7579 (mtm180) REVERT: A 333 GLN cc_start: 0.7529 (tp40) cc_final: 0.7121 (tp-100) REVERT: B 212 ASP cc_start: 0.7579 (t70) cc_final: 0.7157 (t70) REVERT: B 259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7608 (pt0) outliers start: 4 outliers final: 1 residues processed: 154 average time/residue: 1.4621 time to fit residues: 237.3090 Evaluate side-chains 141 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 281 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 GLN R 301 HIS A 188 HIS A 269 ASN A 306 GLN A 331 ASN E 3 GLN E 77 ASN G 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8888 Z= 0.171 Angle : 0.536 7.913 12047 Z= 0.287 Chirality : 0.042 0.145 1382 Planarity : 0.004 0.058 1518 Dihedral : 4.938 64.138 1214 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.36 % Allowed : 12.77 % Favored : 84.87 % 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: 1.43 (0.26), residues: 1097 helix: 2.20 (0.26), residues: 394 sheet: 0.49 (0.30), residues: 280 loop : 0.19 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.005 0.001 HIS R 301 PHE 0.011 0.001 PHE R 72 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 29 LYS cc_start: 0.7844 (tttt) cc_final: 0.7444 (tmmt) REVERT: A 251 ASP cc_start: 0.8201 (t70) cc_final: 0.7926 (t0) REVERT: A 333 GLN cc_start: 0.7685 (tp40) cc_final: 0.7158 (tp-100) REVERT: B 212 ASP cc_start: 0.7400 (t70) cc_final: 0.7035 (OUTLIER) REVERT: B 259 GLN cc_start: 0.7936 (pt0) cc_final: 0.7613 (pt0) REVERT: E 82 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8038 (tp40) REVERT: E 157 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8249 (mp) REVERT: E 160 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.6666 (mtm110) REVERT: E 213 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7785 (t) outliers start: 22 outliers final: 6 residues processed: 166 average time/residue: 1.2769 time to fit residues: 224.8792 Evaluate side-chains 152 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 213 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: 9.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN A 188 HIS A 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8888 Z= 0.187 Angle : 0.525 7.876 12047 Z= 0.275 Chirality : 0.042 0.134 1382 Planarity : 0.004 0.047 1518 Dihedral : 4.555 57.777 1209 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 14.06 % Favored : 83.15 % 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: 1.42 (0.26), residues: 1097 helix: 2.15 (0.26), residues: 401 sheet: 0.45 (0.29), residues: 293 loop : 0.19 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS R 103 PHE 0.010 0.001 PHE E 27 TYR 0.013 0.001 TYR R 183 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: R 79 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8133 (mm) REVERT: R 288 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 21 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7777 (ttm110) REVERT: A 29 LYS cc_start: 0.7826 (tttt) cc_final: 0.7434 (tmmt) REVERT: A 195 HIS cc_start: 0.7227 (m-70) cc_final: 0.7024 (m-70) REVERT: A 242 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7438 (mtm-85) REVERT: A 251 ASP cc_start: 0.8211 (t70) cc_final: 0.7885 (t0) REVERT: A 333 GLN cc_start: 0.7688 (tp40) cc_final: 0.7158 (tp-100) REVERT: B 212 ASP cc_start: 0.7304 (t70) cc_final: 0.6915 (t0) REVERT: B 259 GLN cc_start: 0.7930 (pt0) cc_final: 0.7707 (pt0) REVERT: E 157 ILE cc_start: 0.8576 (mm) cc_final: 0.8217 (mp) outliers start: 26 outliers final: 6 residues processed: 163 average time/residue: 1.2491 time to fit residues: 216.5601 Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.0770 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 269 ASN A 306 GLN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8888 Z= 0.176 Angle : 0.518 7.665 12047 Z= 0.272 Chirality : 0.042 0.155 1382 Planarity : 0.004 0.041 1518 Dihedral : 4.410 53.869 1209 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.47 % Allowed : 15.24 % Favored : 82.30 % 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: 1.42 (0.26), residues: 1097 helix: 2.22 (0.26), residues: 399 sheet: 0.41 (0.29), residues: 292 loop : 0.16 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE R 72 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: R 79 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8158 (mm) REVERT: R 288 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 21 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7729 (ttm110) REVERT: A 29 LYS cc_start: 0.7804 (tttt) cc_final: 0.7402 (tmmt) REVERT: A 333 GLN cc_start: 0.7672 (tp40) cc_final: 0.7192 (tp-100) REVERT: B 197 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7061 (mtt90) REVERT: B 212 ASP cc_start: 0.7239 (t70) cc_final: 0.6855 (t0) REVERT: B 259 GLN cc_start: 0.7912 (pt0) cc_final: 0.7511 (pt0) REVERT: E 157 ILE cc_start: 0.8525 (mm) cc_final: 0.8261 (mp) REVERT: E 178 LEU cc_start: 0.8390 (tp) cc_final: 0.7964 (tp) REVERT: G 21 MET cc_start: 0.6241 (tmm) cc_final: 0.5995 (tpt) outliers start: 23 outliers final: 7 residues processed: 147 average time/residue: 1.3229 time to fit residues: 206.3568 Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 269 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8888 Z= 0.272 Angle : 0.553 6.665 12047 Z= 0.290 Chirality : 0.043 0.149 1382 Planarity : 0.004 0.040 1518 Dihedral : 4.531 50.075 1209 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.36 % Allowed : 16.09 % Favored : 81.55 % 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: 1.36 (0.26), residues: 1097 helix: 2.21 (0.26), residues: 400 sheet: 0.30 (0.30), residues: 278 loop : 0.15 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.011 0.002 PHE R 112 TYR 0.014 0.001 TYR R 107 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 21 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7789 (ttm110) REVERT: A 29 LYS cc_start: 0.7843 (tttt) cc_final: 0.7444 (tmmt) REVERT: A 333 GLN cc_start: 0.7730 (tp40) cc_final: 0.7240 (tp-100) REVERT: B 197 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7079 (mtt90) REVERT: B 212 ASP cc_start: 0.7266 (t70) cc_final: 0.6856 (t70) REVERT: B 259 GLN cc_start: 0.7925 (pt0) cc_final: 0.7459 (pt0) REVERT: E 18 ARG cc_start: 0.7390 (ttm170) cc_final: 0.7146 (ttt90) REVERT: E 157 ILE cc_start: 0.8521 (mm) cc_final: 0.8244 (mp) REVERT: G 21 MET cc_start: 0.6294 (tmm) cc_final: 0.6047 (tpt) REVERT: G 47 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7199 (mp0) REVERT: G 59 ASN cc_start: 0.7883 (t0) cc_final: 0.7632 (t0) outliers start: 22 outliers final: 10 residues processed: 141 average time/residue: 1.5244 time to fit residues: 227.4937 Evaluate side-chains 135 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN A 22 ASN A 269 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8888 Z= 0.203 Angle : 0.524 6.086 12047 Z= 0.276 Chirality : 0.042 0.154 1382 Planarity : 0.004 0.037 1518 Dihedral : 4.445 51.719 1209 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.25 % Allowed : 16.63 % Favored : 81.12 % 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: 1.36 (0.26), residues: 1097 helix: 2.22 (0.26), residues: 402 sheet: 0.32 (0.30), residues: 278 loop : 0.10 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.010 0.001 PHE R 115 TYR 0.013 0.001 TYR R 107 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 21 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7754 (ttm110) REVERT: A 29 LYS cc_start: 0.7818 (tttt) cc_final: 0.7421 (tmmt) REVERT: A 333 GLN cc_start: 0.7732 (tp40) cc_final: 0.7332 (tp-100) REVERT: B 197 ARG cc_start: 0.7659 (mtm110) cc_final: 0.7086 (mtt90) REVERT: B 212 ASP cc_start: 0.7250 (t70) cc_final: 0.6855 (t70) REVERT: B 259 GLN cc_start: 0.7906 (pt0) cc_final: 0.7439 (pt0) REVERT: E 18 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7182 (ttt90) REVERT: E 157 ILE cc_start: 0.8498 (mm) cc_final: 0.8223 (mp) REVERT: E 178 LEU cc_start: 0.8440 (tp) cc_final: 0.8023 (tp) REVERT: G 21 MET cc_start: 0.6327 (tmm) cc_final: 0.6030 (tpt) REVERT: G 47 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7175 (mp0) REVERT: G 59 ASN cc_start: 0.7834 (t0) cc_final: 0.7568 (t0) outliers start: 21 outliers final: 8 residues processed: 143 average time/residue: 1.3733 time to fit residues: 208.2583 Evaluate side-chains 132 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8888 Z= 0.228 Angle : 0.539 5.956 12047 Z= 0.282 Chirality : 0.043 0.162 1382 Planarity : 0.004 0.038 1518 Dihedral : 4.471 53.277 1209 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.04 % Allowed : 17.38 % Favored : 80.58 % 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: 1.38 (0.26), residues: 1097 helix: 2.26 (0.26), residues: 402 sheet: 0.28 (0.29), residues: 284 loop : 0.12 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.011 0.001 PHE R 72 TYR 0.014 0.001 TYR R 30 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8545 (p) REVERT: A 21 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7754 (ttm110) REVERT: A 29 LYS cc_start: 0.7859 (tttt) cc_final: 0.7463 (tmmt) REVERT: A 302 TYR cc_start: 0.7982 (t80) cc_final: 0.7716 (t80) REVERT: A 333 GLN cc_start: 0.7758 (tp40) cc_final: 0.7356 (tp-100) REVERT: B 197 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7107 (mtt90) REVERT: B 212 ASP cc_start: 0.7239 (t70) cc_final: 0.6825 (t70) REVERT: B 259 GLN cc_start: 0.7919 (pt0) cc_final: 0.7447 (pt0) REVERT: E 18 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7143 (ttt90) REVERT: E 157 ILE cc_start: 0.8491 (mm) cc_final: 0.8263 (mp) REVERT: G 21 MET cc_start: 0.6304 (tmm) cc_final: 0.6053 (tpt) REVERT: G 47 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7189 (mp0) REVERT: G 59 ASN cc_start: 0.7826 (t0) cc_final: 0.7554 (t0) outliers start: 19 outliers final: 10 residues processed: 139 average time/residue: 1.3734 time to fit residues: 201.9529 Evaluate side-chains 144 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 269 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.201 Angle : 0.530 6.073 12047 Z= 0.278 Chirality : 0.042 0.177 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.388 51.155 1209 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 18.03 % Favored : 80.04 % 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: 1.42 (0.26), residues: 1097 helix: 2.33 (0.26), residues: 402 sheet: 0.30 (0.29), residues: 284 loop : 0.11 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.010 0.001 PHE R 72 TYR 0.018 0.001 TYR R 30 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.059 Fit side-chains REVERT: R 288 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 21 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7743 (ttm110) REVERT: A 29 LYS cc_start: 0.7838 (tttt) cc_final: 0.7441 (tmmt) REVERT: A 242 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7802 (mtm180) REVERT: A 251 ASP cc_start: 0.8193 (t70) cc_final: 0.7957 (t0) REVERT: A 333 GLN cc_start: 0.7750 (tp40) cc_final: 0.7275 (tp-100) REVERT: A 341 ASP cc_start: 0.7964 (t70) cc_final: 0.7550 (t70) REVERT: A 344 ILE cc_start: 0.7636 (mt) cc_final: 0.7334 (mt) REVERT: B 137 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7168 (ttp-110) REVERT: B 212 ASP cc_start: 0.7239 (t70) cc_final: 0.6831 (t70) REVERT: B 259 GLN cc_start: 0.7923 (pt0) cc_final: 0.7458 (pt0) REVERT: E 3 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: E 18 ARG cc_start: 0.7462 (ttm170) cc_final: 0.7217 (ttt90) REVERT: E 157 ILE cc_start: 0.8530 (mm) cc_final: 0.8211 (mp) REVERT: E 178 LEU cc_start: 0.8433 (tp) cc_final: 0.8031 (tp) REVERT: G 21 MET cc_start: 0.6350 (tmm) cc_final: 0.6081 (tpt) REVERT: G 59 ASN cc_start: 0.7748 (t0) cc_final: 0.7471 (t0) outliers start: 18 outliers final: 10 residues processed: 146 average time/residue: 1.2671 time to fit residues: 196.7715 Evaluate side-chains 136 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 HIS A 22 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8888 Z= 0.193 Angle : 0.532 6.563 12047 Z= 0.278 Chirality : 0.042 0.175 1382 Planarity : 0.004 0.038 1518 Dihedral : 4.328 49.960 1209 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.72 % Allowed : 18.56 % Favored : 79.72 % 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: 1.47 (0.26), residues: 1097 helix: 2.37 (0.26), residues: 403 sheet: 0.32 (0.29), residues: 284 loop : 0.13 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 301 PHE 0.010 0.001 PHE R 72 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.024 Fit side-chains REVERT: R 288 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8592 (p) REVERT: A 21 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7764 (ttm110) REVERT: A 29 LYS cc_start: 0.7833 (tttt) cc_final: 0.7437 (tmmt) REVERT: A 242 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7828 (mtm180) REVERT: A 269 ASN cc_start: 0.8770 (m-40) cc_final: 0.8557 (m110) REVERT: A 333 GLN cc_start: 0.7733 (tp40) cc_final: 0.7330 (tp-100) REVERT: A 344 ILE cc_start: 0.7611 (mt) cc_final: 0.7295 (mt) REVERT: B 212 ASP cc_start: 0.7277 (t70) cc_final: 0.6889 (t70) REVERT: B 217 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6424 (ptt) REVERT: B 259 GLN cc_start: 0.7917 (pt0) cc_final: 0.7440 (pt0) REVERT: E 3 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: E 18 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7220 (ttt90) REVERT: E 93 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7929 (ttm) REVERT: E 157 ILE cc_start: 0.8444 (mm) cc_final: 0.8179 (mp) REVERT: G 21 MET cc_start: 0.6380 (tmm) cc_final: 0.5991 (tpt) REVERT: G 47 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7209 (mp0) REVERT: G 59 ASN cc_start: 0.7748 (t0) cc_final: 0.7465 (t0) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.3415 time to fit residues: 187.9459 Evaluate side-chains 134 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 301 HIS A 22 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8888 Z= 0.147 Angle : 0.506 5.587 12047 Z= 0.267 Chirality : 0.041 0.182 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.160 47.861 1209 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 18.78 % Favored : 79.94 % 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: 1.51 (0.26), residues: 1097 helix: 2.44 (0.26), residues: 404 sheet: 0.33 (0.29), residues: 283 loop : 0.12 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.010 0.001 PHE R 72 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.023 Fit side-chains REVERT: R 288 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 21 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7743 (ttm110) REVERT: A 29 LYS cc_start: 0.7810 (tttt) cc_final: 0.7385 (tmmt) REVERT: A 242 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7792 (mtm180) REVERT: A 308 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 333 GLN cc_start: 0.7724 (tp40) cc_final: 0.7313 (tp-100) REVERT: A 344 ILE cc_start: 0.7540 (mt) cc_final: 0.7131 (mm) REVERT: B 137 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6669 (ttp-170) REVERT: B 153 ASP cc_start: 0.7036 (m-30) cc_final: 0.6431 (p0) REVERT: B 212 ASP cc_start: 0.7259 (t70) cc_final: 0.6849 (t0) REVERT: B 259 GLN cc_start: 0.7917 (pt0) cc_final: 0.7513 (pt0) REVERT: E 3 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: E 18 ARG cc_start: 0.7491 (ttm170) cc_final: 0.7240 (ttt90) REVERT: E 93 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7935 (ttm) REVERT: E 158 SER cc_start: 0.8864 (p) cc_final: 0.8544 (t) REVERT: E 178 LEU cc_start: 0.8400 (tp) cc_final: 0.8049 (tp) REVERT: G 47 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7160 (mp0) REVERT: G 58 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7058 (tm-30) REVERT: G 59 ASN cc_start: 0.7807 (t0) cc_final: 0.7605 (t0) outliers start: 12 outliers final: 7 residues processed: 138 average time/residue: 1.3102 time to fit residues: 192.2896 Evaluate side-chains 144 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 301 HIS A 22 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114243 restraints weight = 10797.456| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.39 r_work: 0.3337 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8888 Z= 0.167 Angle : 0.516 6.581 12047 Z= 0.270 Chirality : 0.042 0.178 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.144 47.405 1209 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.18 % Allowed : 19.31 % Favored : 79.51 % 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: 1.52 (0.26), residues: 1097 helix: 2.46 (0.26), residues: 403 sheet: 0.33 (0.29), residues: 283 loop : 0.12 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 301 PHE 0.011 0.001 PHE R 72 TYR 0.028 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.04 seconds wall clock time: 73 minutes 8.45 seconds (4388.45 seconds total)