Starting phenix.real_space_refine on Fri Jul 19 16:53:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/07_2024/8ykx_39375_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/07_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_39375/07_2024/8ykx_39375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/07_2024/8ykx_39375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/07_2024/8ykx_39375_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/07_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-5388/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: 5.40, 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: 3.90 Conformation dependent library (CDL) restraints added in 1.6 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: 1.08 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: 2.87 Time building geometry restraints manager: 4.20 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 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.305 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.312 2.440 nonbonded pdb=" O GLY R 37 " pdb=" ND2 ASN R 41 " model vdw 2.351 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.500 Find NCS groups from input model: 0.090 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- 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 : 1.052 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: 1.5105 time to fit residues: 245.4287 Evaluate side-chains 141 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1141 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= 0.163 Angle : 0.518 7.699 12047 Z= 0.275 Chirality : 0.041 0.141 1382 Planarity : 0.004 0.055 1518 Dihedral : 5.111 85.817 1214 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.04 % Allowed : 13.52 % Favored : 84.44 % 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: 1.44 (0.26), residues: 1097 helix: 2.22 (0.27), residues: 392 sheet: 0.48 (0.30), residues: 279 loop : 0.20 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS R 301 PHE 0.011 0.001 PHE R 72 TYR 0.013 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 166 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 203 MET cc_start: 0.8480 (ttm) cc_final: 0.8279 (mtp) REVERT: R 288 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 29 LYS cc_start: 0.7845 (tttt) cc_final: 0.7441 (tmmt) REVERT: A 251 ASP cc_start: 0.8165 (t70) cc_final: 0.7916 (t0) REVERT: A 306 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: A 333 GLN cc_start: 0.7586 (tp40) cc_final: 0.7124 (tp-100) REVERT: B 212 ASP cc_start: 0.7419 (t70) cc_final: 0.7054 (OUTLIER) REVERT: B 259 GLN cc_start: 0.7947 (pt0) cc_final: 0.7491 (pt0) REVERT: E 157 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8342 (mp) REVERT: E 160 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6614 (mtm110) REVERT: E 163 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7682 (ttpt) outliers start: 19 outliers final: 5 residues processed: 153 average time/residue: 1.3411 time to fit residues: 217.3714 Evaluate side-chains 138 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 288 SER Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 82 GLN G 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8888 Z= 0.163 Angle : 0.506 7.740 12047 Z= 0.266 Chirality : 0.041 0.131 1382 Planarity : 0.004 0.042 1518 Dihedral : 4.805 85.873 1209 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.68 % Allowed : 14.38 % Favored : 82.94 % 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: 1.46 (0.26), residues: 1097 helix: 2.21 (0.26), residues: 398 sheet: 0.42 (0.29), residues: 292 loop : 0.26 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE R 72 TYR 0.011 0.001 TYR E 190 ARG 0.008 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 173 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8061 (mm) REVERT: R 288 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8506 (p) REVERT: A 29 LYS cc_start: 0.7819 (tttt) cc_final: 0.7418 (tmmt) REVERT: A 251 ASP cc_start: 0.8173 (t70) cc_final: 0.7904 (t0) REVERT: A 333 GLN cc_start: 0.7626 (tp40) cc_final: 0.7090 (tp-100) REVERT: B 212 ASP cc_start: 0.7380 (t70) cc_final: 0.6974 (t0) REVERT: B 259 GLN cc_start: 0.7946 (pt0) cc_final: 0.7475 (pt0) REVERT: E 157 ILE cc_start: 0.8594 (mm) cc_final: 0.8324 (mp) outliers start: 25 outliers final: 5 residues processed: 159 average time/residue: 1.2434 time to fit residues: 210.4035 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 188 HIS A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8888 Z= 0.281 Angle : 0.553 7.775 12047 Z= 0.289 Chirality : 0.044 0.148 1382 Planarity : 0.004 0.042 1518 Dihedral : 4.957 85.269 1209 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 16.85 % 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: 1.31 (0.26), residues: 1097 helix: 2.16 (0.26), residues: 394 sheet: 0.31 (0.30), residues: 277 loop : 0.13 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS R 103 PHE 0.012 0.002 PHE A 196 TYR 0.014 0.001 TYR R 107 ARG 0.009 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 158 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.037 Fit side-chains REVERT: R 288 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 29 LYS cc_start: 0.7861 (tttt) cc_final: 0.7456 (tmmt) REVERT: A 333 GLN cc_start: 0.7652 (tp40) cc_final: 0.7168 (tp-100) REVERT: B 212 ASP cc_start: 0.7324 (t70) cc_final: 0.6890 (t70) REVERT: B 259 GLN cc_start: 0.7962 (pt0) cc_final: 0.7460 (pt0) REVERT: E 157 ILE cc_start: 0.8568 (mm) cc_final: 0.8282 (mp) REVERT: G 21 MET cc_start: 0.6254 (tmm) cc_final: 0.5988 (tpt) outliers start: 24 outliers final: 11 residues processed: 149 average time/residue: 1.3323 time to fit residues: 210.3422 Evaluate side-chains 142 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 ASN 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 A residue 48 THR 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 83 MET Chi-restraints excluded: chain E residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8888 Z= 0.335 Angle : 0.579 7.154 12047 Z= 0.302 Chirality : 0.045 0.167 1382 Planarity : 0.004 0.041 1518 Dihedral : 5.096 84.057 1209 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.79 % Allowed : 17.06 % Favored : 80.15 % 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: 1.15 (0.26), residues: 1097 helix: 2.03 (0.26), residues: 394 sheet: 0.16 (0.29), residues: 287 loop : 0.09 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS R 103 PHE 0.013 0.002 PHE R 112 TYR 0.015 0.002 TYR R 107 ARG 0.007 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 158 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: R 152 LEU cc_start: 0.7684 (mt) cc_final: 0.7446 (mp) REVERT: R 288 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 29 LYS cc_start: 0.7886 (tttt) cc_final: 0.7469 (tmmt) REVERT: A 242 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7514 (mtm180) REVERT: A 333 GLN cc_start: 0.7662 (tp40) cc_final: 0.7187 (tp-100) REVERT: B 212 ASP cc_start: 0.7363 (t70) cc_final: 0.6864 (t70) REVERT: B 259 GLN cc_start: 0.8001 (pt0) cc_final: 0.7570 (pt0) REVERT: E 157 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8228 (mp) outliers start: 26 outliers final: 11 residues processed: 143 average time/residue: 1.3725 time to fit residues: 208.1255 Evaluate side-chains 137 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 A residue 48 THR 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 83 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 306 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1863 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= 0.183 Angle : 0.510 6.522 12047 Z= 0.268 Chirality : 0.042 0.161 1382 Planarity : 0.004 0.036 1518 Dihedral : 4.828 85.387 1209 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.68 % Allowed : 17.60 % 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: 1.30 (0.26), residues: 1097 helix: 2.21 (0.26), residues: 396 sheet: 0.23 (0.29), residues: 281 loop : 0.11 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 103 PHE 0.010 0.001 PHE R 34 TYR 0.013 0.001 TYR R 30 ARG 0.009 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 163 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 29 LYS cc_start: 0.7839 (tttt) cc_final: 0.7412 (tmmt) REVERT: A 242 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7510 (mtm180) REVERT: A 333 GLN cc_start: 0.7653 (tp40) cc_final: 0.7173 (tp-100) REVERT: B 212 ASP cc_start: 0.7240 (t70) cc_final: 0.6827 (t70) REVERT: B 259 GLN cc_start: 0.7951 (pt0) cc_final: 0.7464 (pt0) REVERT: B 304 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7487 (ttm170) REVERT: E 3 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: E 18 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7276 (ttt90) REVERT: E 157 ILE cc_start: 0.8481 (mm) cc_final: 0.8214 (mp) REVERT: G 59 ASN cc_start: 0.7840 (t0) cc_final: 0.7612 (t0) outliers start: 25 outliers final: 10 residues processed: 151 average time/residue: 1.3844 time to fit residues: 221.1352 Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 ASN 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 A residue 48 THR Chi-restraints excluded: chain A residue 182 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 306 GLN E 39 GLN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8888 Z= 0.193 Angle : 0.518 6.366 12047 Z= 0.272 Chirality : 0.042 0.162 1382 Planarity : 0.004 0.036 1518 Dihedral : 4.744 83.590 1209 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.58 % Allowed : 18.56 % Favored : 78.86 % 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: 1.35 (0.26), residues: 1097 helix: 2.21 (0.26), residues: 402 sheet: 0.30 (0.29), residues: 277 loop : 0.12 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 R 107 ARG 0.008 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 165 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.051 Fit side-chains REVERT: R 288 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 24 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7451 (ptp90) REVERT: A 29 LYS cc_start: 0.7824 (tttt) cc_final: 0.7418 (tmmt) REVERT: A 251 ASP cc_start: 0.8184 (t70) cc_final: 0.7905 (t0) REVERT: A 306 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: A 333 GLN cc_start: 0.7678 (tp40) cc_final: 0.7164 (tp-100) REVERT: B 212 ASP cc_start: 0.7252 (t70) cc_final: 0.6841 (t70) REVERT: B 259 GLN cc_start: 0.7961 (pt0) cc_final: 0.7472 (pt0) REVERT: E 18 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7291 (ttt90) REVERT: E 38 ARG cc_start: 0.8486 (ptm160) cc_final: 0.8252 (ptp-170) REVERT: E 157 ILE cc_start: 0.8459 (mm) cc_final: 0.8195 (mp) REVERT: G 21 MET cc_start: 0.6307 (tmm) cc_final: 0.6052 (tpt) REVERT: G 59 ASN cc_start: 0.7797 (t0) cc_final: 0.7588 (t0) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 1.3080 time to fit residues: 216.4151 Evaluate side-chains 150 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 306 GLN 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 228 ASP Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4300 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8888 Z= 0.137 Angle : 0.495 6.623 12047 Z= 0.259 Chirality : 0.041 0.173 1382 Planarity : 0.004 0.038 1518 Dihedral : 4.611 85.046 1209 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.15 % Allowed : 19.42 % Favored : 78.43 % 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: 2.32 (0.26), residues: 402 sheet: 0.38 (0.30), residues: 275 loop : 0.15 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 301 PHE 0.010 0.001 PHE R 34 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 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 154 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.022 Fit side-chains REVERT: A 29 LYS cc_start: 0.7808 (tttt) cc_final: 0.7415 (tmmt) REVERT: A 242 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7403 (mtm180) REVERT: A 251 ASP cc_start: 0.8153 (t70) cc_final: 0.7868 (t0) REVERT: B 212 ASP cc_start: 0.7205 (t70) cc_final: 0.6837 (t70) REVERT: B 217 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6349 (ptt) REVERT: B 259 GLN cc_start: 0.7941 (pt0) cc_final: 0.7453 (pt0) REVERT: E 18 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7266 (ttt90) REVERT: E 38 ARG cc_start: 0.8457 (ptm160) cc_final: 0.8245 (ptp-170) REVERT: E 93 MET cc_start: 0.8373 (ttp) cc_final: 0.7941 (ttm) REVERT: E 157 ILE cc_start: 0.8423 (mm) cc_final: 0.8175 (mp) REVERT: G 21 MET cc_start: 0.6327 (tmm) cc_final: 0.5923 (tpt) outliers start: 20 outliers final: 10 residues processed: 149 average time/residue: 1.2932 time to fit residues: 204.5245 Evaluate side-chains 138 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 233 VAL 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 228 ASP Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.0010 chunk 63 optimal weight: 0.7980 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8888 Z= 0.186 Angle : 0.518 7.816 12047 Z= 0.272 Chirality : 0.042 0.178 1382 Planarity : 0.004 0.038 1518 Dihedral : 4.637 84.828 1209 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 20.17 % Favored : 78.00 % 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: 2.34 (0.26), residues: 403 sheet: 0.44 (0.30), residues: 275 loop : 0.17 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 R 107 ARG 0.009 0.000 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 152 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.063 Fit side-chains REVERT: A 29 LYS cc_start: 0.7800 (tttt) cc_final: 0.7406 (tmmt) REVERT: A 242 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7570 (mtm180) REVERT: A 251 ASP cc_start: 0.8159 (t70) cc_final: 0.7870 (t0) REVERT: A 330 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.4660 (mptt) REVERT: B 212 ASP cc_start: 0.7231 (t70) cc_final: 0.6831 (t70) REVERT: B 217 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6382 (ptt) REVERT: B 259 GLN cc_start: 0.7962 (pt0) cc_final: 0.7530 (pt0) REVERT: E 18 ARG cc_start: 0.7490 (ttm170) cc_final: 0.7158 (ttt90) REVERT: E 38 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8255 (ptp-170) REVERT: E 157 ILE cc_start: 0.8415 (mm) cc_final: 0.8165 (mp) REVERT: G 21 MET cc_start: 0.6336 (tmm) cc_final: 0.5935 (tpt) REVERT: G 59 ASN cc_start: 0.7782 (t0) cc_final: 0.7554 (t0) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 1.3029 time to fit residues: 202.0292 Evaluate side-chains 147 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 233 VAL 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 228 ASP Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 100 optimal weight: 0.0000 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7912 moved from start: 0.2232 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= 0.175 Angle : 0.511 7.563 12047 Z= 0.266 Chirality : 0.042 0.184 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.618 84.927 1209 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.72 % Allowed : 20.49 % Favored : 77.79 % 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: 1.53 (0.26), residues: 1097 helix: 2.38 (0.26), residues: 403 sheet: 0.35 (0.30), residues: 280 loop : 0.23 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 R 107 ARG 0.009 0.000 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 151 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.011 Fit side-chains REVERT: A 29 LYS cc_start: 0.7790 (tttt) cc_final: 0.7375 (tmmt) REVERT: A 242 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7565 (mtm180) REVERT: A 251 ASP cc_start: 0.8169 (t70) cc_final: 0.7913 (t0) REVERT: A 270 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8112 (mmmm) REVERT: A 308 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 333 GLN cc_start: 0.7668 (tp40) cc_final: 0.7182 (tp-100) REVERT: A 344 ILE cc_start: 0.7650 (mt) cc_final: 0.7312 (mt) REVERT: B 212 ASP cc_start: 0.7242 (t70) cc_final: 0.6839 (t70) REVERT: B 217 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6377 (ptt) REVERT: B 259 GLN cc_start: 0.7982 (pt0) cc_final: 0.7596 (pt0) REVERT: E 18 ARG cc_start: 0.7451 (ttm170) cc_final: 0.7203 (ttt90) REVERT: E 157 ILE cc_start: 0.8436 (mm) cc_final: 0.8193 (mp) REVERT: G 21 MET cc_start: 0.6340 (tmm) cc_final: 0.5966 (tpt) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 1.3076 time to fit residues: 201.4481 Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain R residue 236 MET Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 301 HIS A 269 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114880 restraints weight = 10790.788| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.41 r_work: 0.3341 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8888 Z= 0.143 Angle : 0.504 9.204 12047 Z= 0.264 Chirality : 0.041 0.185 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.517 85.356 1209 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.18 % Allowed : 21.35 % Favored : 77.47 % 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: 1.58 (0.26), residues: 1097 helix: 2.44 (0.26), residues: 404 sheet: 0.33 (0.29), residues: 280 loop : 0.26 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 301 PHE 0.010 0.001 PHE R 34 TYR 0.011 0.001 TYR E 190 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: 4187.89 seconds wall clock time: 73 minutes 38.33 seconds (4418.33 seconds total)