Starting phenix.real_space_refine on Wed Feb 14 08:34:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/02_2024/6wzg_21972.pdb" } resolution = 2.3 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= 0.000 sd= 0.004 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 57 5.16 5 C 5643 2.51 5 N 1592 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 15": "OE1" <-> "OE2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R ARG 135": "NH1" <-> "NH2" Residue "R ARG 169": "NH1" <-> "NH2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R GLU 281": "OE1" <-> "OE2" Residue "R GLU 328": "OE1" <-> "OE2" Residue "R GLU 333": "OE1" <-> "OE2" Residue "R GLU 363": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8939 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2781 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 11, 'TRANS': 367} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1960 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 8939 At special positions: 0 Unit cell: (94.62, 100.43, 161.02, 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 57 16.00 O 1647 8.00 N 1592 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.04 Simple disulfide: pdb=" SG CYS R 66 " - pdb=" SG CYS R 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.05 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 42.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'P' and resid 1 through 27 removed outlier: 3.518A pdb=" N LEU P 22 " --> pdb=" O ARG P 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 48 Processing helix chain 'R' and resid 90 through 95 removed outlier: 3.934A pdb=" N MET R 95 " --> pdb=" O ARG R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 167 removed outlier: 3.587A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 201 removed outlier: 3.601A pdb=" N SER R 201 " --> pdb=" O ALA R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 254 through 280 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 291 through 326 removed outlier: 3.750A pdb=" N ILE R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 332 through 352 Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 354 through 359 removed outlier: 4.474A pdb=" N PHE R 358 " --> pdb=" O HIS R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 364 No H-bonds generated for 'chain 'R' and resid 362 through 364' Processing helix chain 'R' and resid 365 through 375 Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 389 Processing helix chain 'R' and resid 392 through 408 Processing helix chain 'A' and resid 13 through 40 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.611A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.700A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.744A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.002A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.972A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.729A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.874A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.600A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.972A 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: 6.611A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A 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: 6.120A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1347 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: 2.73 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1473 1.29 - 1.43: 2428 1.43 - 1.56: 5133 1.56 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 9112 Sorted by residual: bond pdb=" C HIS R 178 " pdb=" O HIS R 178 " ideal model delta sigma weight residual 1.237 1.164 0.072 1.17e-02 7.31e+03 3.82e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.60e-03 1.73e+04 2.09e+01 bond pdb=" C ILE R 297 " pdb=" O ILE R 297 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.23e-02 6.61e+03 2.07e+01 bond pdb=" C ARG R 174 " pdb=" O ARG R 174 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" C ILE R 298 " pdb=" O ILE R 298 " ideal model delta sigma weight residual 1.231 1.187 0.044 1.07e-02 8.73e+03 1.66e+01 ... (remaining 9107 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.95: 270 106.95 - 113.83: 4885 113.83 - 120.70: 4273 120.70 - 127.57: 2839 127.57 - 134.45: 72 Bond angle restraints: 12339 Sorted by residual: angle pdb=" N SER R 74 " pdb=" CA SER R 74 " pdb=" C SER R 74 " ideal model delta sigma weight residual 111.07 102.97 8.10 1.07e+00 8.73e-01 5.73e+01 angle pdb=" N ASP R 209 " pdb=" CA ASP R 209 " pdb=" C ASP R 209 " ideal model delta sigma weight residual 114.39 103.87 10.52 1.45e+00 4.76e-01 5.26e+01 angle pdb=" C THR R 326 " pdb=" CA THR R 326 " pdb=" CB THR R 326 " ideal model delta sigma weight residual 111.74 101.83 9.91 1.37e+00 5.33e-01 5.23e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.02 105.22 7.80 1.20e+00 6.94e-01 4.23e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 113.02 105.42 7.60 1.20e+00 6.94e-01 4.01e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4919 17.92 - 35.84: 406 35.84 - 53.76: 70 53.76 - 71.67: 22 71.67 - 89.59: 7 Dihedral angle restraints: 5424 sinusoidal: 2048 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS R 89 " pdb=" SG CYS R 89 " pdb=" SG CYS R 123 " pdb=" CB CYS R 123 " ideal model delta sinusoidal sigma weight residual 93.00 169.26 -76.26 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" C TYR R 146 " pdb=" N TYR R 146 " pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " ideal model delta harmonic sigma weight residual -122.60 -138.79 16.19 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.19 52.81 1 1.00e+01 1.00e-02 3.80e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 870 0.108 - 0.216: 435 0.216 - 0.324: 65 0.324 - 0.432: 13 0.432 - 0.540: 4 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA TYR R 146 " pdb=" N TYR R 146 " pdb=" C TYR R 146 " pdb=" CB TYR R 146 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA ASN R 175 " pdb=" N ASN R 175 " pdb=" C ASN R 175 " pdb=" CB ASN R 175 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CA TRP A 234 " pdb=" N TRP A 234 " pdb=" C TRP A 234 " pdb=" CB TRP A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 1384 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C SER A 205 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 206 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 277 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C TRP A 277 " 0.055 2.00e-02 2.50e+03 pdb=" O TRP A 277 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 278 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 332 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C TRP B 332 " 0.051 2.00e-02 2.50e+03 pdb=" O TRP B 332 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP B 333 " -0.017 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1630 2.80 - 3.32: 9004 3.32 - 3.85: 14916 3.85 - 4.37: 19498 4.37 - 4.90: 30896 Nonbonded interactions: 75944 Sorted by model distance: nonbonded pdb=" OG SER A 205 " pdb=" O ILE A 207 " model vdw 2.270 2.440 nonbonded pdb=" N GLU R 251 " pdb=" OE1 GLU R 251 " model vdw 2.276 2.520 nonbonded pdb=" N VAL R 85 " pdb=" O LEU R 103 " model vdw 2.377 2.520 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.392 2.520 nonbonded pdb=" O GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.394 2.520 ... (remaining 75939 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=0.00 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: 0.000 Extract box with map and model: 5.250 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.490 Find NCS groups from input model: 0.280 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.012 0.072 9112 Z= 0.796 Angle : 1.561 10.517 12339 Z= 1.199 Chirality : 0.121 0.540 1387 Planarity : 0.007 0.034 1589 Dihedral : 14.021 89.594 3224 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 9.35 % Favored : 89.00 % Cbeta Deviations : 1.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1151 helix: 1.41 (0.24), residues: 453 sheet: 0.76 (0.34), residues: 208 loop : -0.32 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 232 HIS 0.007 0.002 HIS A 41 PHE 0.022 0.002 PHE G 61 TYR 0.018 0.002 TYR R 146 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: R 321 MET cc_start: 0.6158 (tpt) cc_final: 0.5830 (mmm) REVERT: A 17 LYS cc_start: 0.6608 (pttp) cc_final: 0.6228 (tppt) REVERT: A 357 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8263 (p90) REVERT: B 124 TYR cc_start: 0.8512 (m-80) cc_final: 0.8310 (m-80) outliers start: 15 outliers final: 3 residues processed: 178 average time/residue: 1.4951 time to fit residues: 280.4223 Evaluate side-chains 129 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 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 132 ASN R 178 HIS R 180 HIS R 229 ASN R 327 GLN R 354 HIS R 396 GLN R 404 GLN A 220 HIS A 362 HIS A 390 GLN B 35 ASN B 259 GLN B 340 ASN N 1 GLN N 3 GLN N 120 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9112 Z= 0.183 Angle : 0.566 7.056 12339 Z= 0.318 Chirality : 0.043 0.140 1387 Planarity : 0.004 0.037 1589 Dihedral : 4.965 51.540 1273 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.70 % Rotamer: Outliers : 2.75 % Allowed : 13.75 % Favored : 83.50 % 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: 1.55 (0.24), residues: 1151 helix: 2.35 (0.23), residues: 461 sheet: 0.79 (0.33), residues: 217 loop : -0.15 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R 407 PHE 0.020 0.002 PHE G 61 TYR 0.026 0.002 TYR R 146 ARG 0.004 0.001 ARG R 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8012 (pttp) outliers start: 25 outliers final: 7 residues processed: 160 average time/residue: 1.5330 time to fit residues: 259.5648 Evaluate side-chains 134 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 111 optimal weight: 0.0040 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 35 ASN B 259 GLN B 340 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9112 Z= 0.182 Angle : 0.531 5.882 12339 Z= 0.299 Chirality : 0.042 0.144 1387 Planarity : 0.004 0.038 1589 Dihedral : 4.887 56.880 1267 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.86 % Allowed : 14.74 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1151 helix: 2.74 (0.23), residues: 461 sheet: 0.69 (0.33), residues: 217 loop : -0.15 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 PHE 0.019 0.002 PHE R 313 TYR 0.027 0.002 TYR R 146 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.014 Fit side-chains REVERT: R 123 CYS cc_start: -0.1175 (OUTLIER) cc_final: -0.1635 (t) REVERT: A 31 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7132 (tp40) REVERT: A 53 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8023 (pttp) outliers start: 26 outliers final: 11 residues processed: 142 average time/residue: 1.4996 time to fit residues: 224.4951 Evaluate side-chains 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 35 ASN B 268 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9112 Z= 0.175 Angle : 0.511 5.459 12339 Z= 0.288 Chirality : 0.041 0.142 1387 Planarity : 0.004 0.038 1589 Dihedral : 4.883 59.793 1267 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.19 % Allowed : 14.41 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1151 helix: 2.74 (0.23), residues: 467 sheet: 0.53 (0.33), residues: 219 loop : -0.19 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 PHE 0.018 0.002 PHE R 313 TYR 0.025 0.002 TYR R 146 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.100 Fit side-chains REVERT: R 123 CYS cc_start: -0.0901 (OUTLIER) cc_final: -0.1297 (t) REVERT: A 31 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: A 53 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8037 (pttp) REVERT: A 59 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6469 (pt0) REVERT: B 325 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7273 (tpp) outliers start: 29 outliers final: 12 residues processed: 141 average time/residue: 1.6567 time to fit residues: 245.7570 Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 CYS Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 387 HIS B 35 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9112 Z= 0.150 Angle : 0.484 5.485 12339 Z= 0.273 Chirality : 0.041 0.141 1387 Planarity : 0.003 0.039 1589 Dihedral : 4.722 57.017 1267 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.64 % Allowed : 14.85 % Favored : 82.51 % 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: 1.79 (0.25), residues: 1151 helix: 2.89 (0.24), residues: 461 sheet: 0.49 (0.33), residues: 219 loop : -0.19 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.003 0.001 HIS R 241 PHE 0.017 0.002 PHE R 313 TYR 0.024 0.001 TYR R 146 ARG 0.003 0.000 ARG R 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.066 Fit side-chains REVERT: R 123 CYS cc_start: -0.0928 (OUTLIER) cc_final: -0.1313 (t) REVERT: R 325 ARG cc_start: 0.5785 (OUTLIER) cc_final: 0.5126 (mpt-90) REVERT: R 339 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5950 (tpm-80) REVERT: A 31 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7157 (tp40) REVERT: A 53 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8052 (pttp) REVERT: B 325 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7273 (tpp) outliers start: 24 outliers final: 9 residues processed: 140 average time/residue: 1.5005 time to fit residues: 221.6729 Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 267 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9112 Z= 0.248 Angle : 0.565 5.955 12339 Z= 0.318 Chirality : 0.043 0.142 1387 Planarity : 0.004 0.040 1589 Dihedral : 5.063 54.393 1267 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.31 % Allowed : 14.85 % Favored : 82.84 % 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: 1.53 (0.24), residues: 1151 helix: 2.60 (0.23), residues: 461 sheet: 0.31 (0.33), residues: 222 loop : -0.22 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS R 241 PHE 0.020 0.002 PHE R 313 TYR 0.024 0.002 TYR R 146 ARG 0.003 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.045 Fit side-chains REVERT: R 123 CYS cc_start: -0.0960 (OUTLIER) cc_final: -0.1304 (t) REVERT: A 31 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7161 (tp40) REVERT: A 53 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (pttp) REVERT: A 59 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6469 (pt0) REVERT: B 325 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7327 (tpp) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 1.5626 time to fit residues: 223.9850 Evaluate side-chains 133 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9112 Z= 0.147 Angle : 0.483 5.555 12339 Z= 0.274 Chirality : 0.040 0.141 1387 Planarity : 0.003 0.040 1589 Dihedral : 4.728 53.171 1267 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 15.07 % Favored : 82.18 % 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: 1.73 (0.25), residues: 1151 helix: 2.84 (0.24), residues: 461 sheet: 0.34 (0.33), residues: 219 loop : -0.16 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS R 241 PHE 0.017 0.001 PHE R 313 TYR 0.023 0.001 TYR R 146 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.989 Fit side-chains REVERT: R 325 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5106 (mpt-90) REVERT: R 339 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5940 (tpm-80) REVERT: A 31 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7142 (tp40) REVERT: A 59 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6457 (pt0) REVERT: B 325 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7350 (tpp) outliers start: 25 outliers final: 9 residues processed: 139 average time/residue: 1.5961 time to fit residues: 233.3280 Evaluate side-chains 136 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 50.0000 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9112 Z= 0.212 Angle : 0.535 5.733 12339 Z= 0.301 Chirality : 0.042 0.139 1387 Planarity : 0.004 0.040 1589 Dihedral : 4.663 22.194 1266 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.20 % Allowed : 15.84 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1151 helix: 2.68 (0.24), residues: 455 sheet: 0.30 (0.33), residues: 211 loop : -0.21 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS R 241 PHE 0.019 0.002 PHE R 313 TYR 0.023 0.002 TYR R 146 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.069 Fit side-chains REVERT: R 325 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5144 (mpt-90) REVERT: A 31 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7146 (tp40) REVERT: A 314 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7035 (pm20) REVERT: B 325 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7342 (tpp) outliers start: 20 outliers final: 10 residues processed: 132 average time/residue: 1.7037 time to fit residues: 237.0473 Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 CYS Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9112 Z= 0.291 Angle : 0.602 6.421 12339 Z= 0.338 Chirality : 0.045 0.145 1387 Planarity : 0.005 0.041 1589 Dihedral : 4.973 24.374 1266 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.53 % Allowed : 15.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1151 helix: 2.32 (0.23), residues: 455 sheet: 0.21 (0.33), residues: 213 loop : -0.27 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.007 0.001 HIS A 41 PHE 0.021 0.002 PHE R 313 TYR 0.026 0.002 TYR A 339 ARG 0.008 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.108 Fit side-chains REVERT: R 325 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5154 (mpt-90) REVERT: A 314 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6957 (pm20) REVERT: B 325 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7370 (tpp) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 1.6051 time to fit residues: 227.6871 Evaluate side-chains 132 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 89 optimal weight: 0.4980 chunk 9 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 GLN A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9112 Z= 0.161 Angle : 0.499 5.553 12339 Z= 0.281 Chirality : 0.041 0.142 1387 Planarity : 0.004 0.040 1589 Dihedral : 4.543 20.444 1266 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.65 % Allowed : 16.17 % Favored : 82.18 % 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 (0.25), residues: 1151 helix: 2.77 (0.24), residues: 449 sheet: 0.28 (0.33), residues: 221 loop : -0.22 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS R 241 PHE 0.017 0.002 PHE R 313 TYR 0.023 0.002 TYR R 146 ARG 0.007 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.132 Fit side-chains REVERT: R 325 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5050 (mpt-90) REVERT: B 325 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7361 (tpp) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 1.6302 time to fit residues: 226.6670 Evaluate side-chains 129 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 64 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116232 restraints weight = 8073.297| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.41 r_work: 0.3142 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9112 Z= 0.224 Angle : 0.550 6.108 12339 Z= 0.309 Chirality : 0.042 0.142 1387 Planarity : 0.004 0.045 1589 Dihedral : 4.730 22.649 1266 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.54 % Allowed : 16.28 % Favored : 82.18 % 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 (0.24), residues: 1151 helix: 2.61 (0.24), residues: 449 sheet: 0.24 (0.33), residues: 211 loop : -0.28 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.019 0.002 PHE R 313 TYR 0.023 0.002 TYR R 146 ARG 0.008 0.001 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.07 seconds wall clock time: 78 minutes 11.43 seconds (4691.43 seconds total)