Starting phenix.real_space_refine on Fri Dec 8 18:38:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/12_2023/6wzg_21972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/12_2023/6wzg_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_21972/12_2023/6wzg_21972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/12_2023/6wzg_21972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/12_2023/6wzg_21972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wzg_21972/12_2023/6wzg_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.80, per 1000 atoms: 0.54 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 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: 0.98 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: 2.40 Time building geometry restraints manager: 3.48 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: 1.150 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: 5.270 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- 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 : 1.048 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 178 average time/residue: 1.5220 time to fit residues: 285.5387 Evaluate side-chains 128 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6873 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9112 Z= 0.181 Angle : 0.572 6.974 12339 Z= 0.319 Chirality : 0.043 0.143 1387 Planarity : 0.004 0.038 1589 Dihedral : 4.660 19.459 1266 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.70 % Rotamer: Outliers : 2.86 % Allowed : 13.64 % 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: 1.56 (0.24), residues: 1151 helix: 2.36 (0.23), residues: 461 sheet: 0.81 (0.33), residues: 217 loop : -0.15 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE G 61 TYR 0.015 0.002 TYR R 146 ARG 0.005 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 168 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 162 average time/residue: 1.5014 time to fit residues: 256.7318 Evaluate side-chains 138 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.0706 time to fit residues: 3.7688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 111 optimal weight: 0.0020 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.168 Angle : 0.523 5.933 12339 Z= 0.294 Chirality : 0.042 0.142 1387 Planarity : 0.004 0.038 1589 Dihedral : 4.540 18.657 1266 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.08 % Allowed : 14.52 % 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: 1.82 (0.25), residues: 1151 helix: 2.80 (0.23), residues: 461 sheet: 0.71 (0.33), residues: 217 loop : -0.14 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 PHE 0.018 0.002 PHE R 313 TYR 0.020 0.002 TYR R 146 ARG 0.006 0.000 ARG P 18 *********************** 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 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 141 average time/residue: 1.6156 time to fit residues: 239.6642 Evaluate side-chains 134 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0812 time to fit residues: 1.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.0470 chunk 49 optimal weight: 30.0000 chunk 69 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9112 Z= 0.161 Angle : 0.500 5.718 12339 Z= 0.280 Chirality : 0.041 0.143 1387 Planarity : 0.003 0.039 1589 Dihedral : 4.459 18.558 1266 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.30 % Allowed : 14.30 % 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: 1.82 (0.25), residues: 1151 helix: 2.85 (0.23), residues: 467 sheet: 0.57 (0.33), residues: 219 loop : -0.17 (0.28), residues: 465 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 0.021 0.002 TYR R 146 ARG 0.004 0.000 ARG R 135 *********************** 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 160 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.117 Fit side-chains outliers start: 30 outliers final: 11 residues processed: 147 average time/residue: 1.5198 time to fit residues: 235.6859 Evaluate side-chains 136 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.7752 time to fit residues: 3.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9112 Z= 0.179 Angle : 0.516 5.728 12339 Z= 0.290 Chirality : 0.041 0.142 1387 Planarity : 0.004 0.040 1589 Dihedral : 4.553 20.659 1266 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 15.18 % Favored : 82.73 % 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: 2.87 (0.23), residues: 461 sheet: 0.45 (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 0.005 0.001 HIS R 241 PHE 0.018 0.002 PHE R 313 TYR 0.022 0.002 TYR R 146 ARG 0.004 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 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.965 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 136 average time/residue: 1.5337 time to fit residues: 220.2037 Evaluate side-chains 131 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.4767 time to fit residues: 2.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 GLN A 267 GLN B 35 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9112 Z= 0.337 Angle : 0.643 6.772 12339 Z= 0.360 Chirality : 0.047 0.150 1387 Planarity : 0.005 0.043 1589 Dihedral : 5.115 25.857 1266 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.42 % Allowed : 14.19 % Favored : 83.39 % 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: 2.25 (0.23), residues: 461 sheet: 0.28 (0.33), residues: 213 loop : -0.28 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 234 HIS 0.008 0.002 HIS R 241 PHE 0.021 0.003 PHE R 313 TYR 0.027 0.003 TYR A 339 ARG 0.005 0.001 ARG B 251 *********************** 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: 22 poor density : 120 time to evaluate : 1.006 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 136 average time/residue: 1.5309 time to fit residues: 219.8283 Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.3078 time to fit residues: 5.6478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 266 HIS B 268 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9112 Z= 0.192 Angle : 0.523 5.719 12339 Z= 0.296 Chirality : 0.042 0.143 1387 Planarity : 0.004 0.041 1589 Dihedral : 4.728 22.715 1266 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.98 % Allowed : 15.29 % Favored : 82.73 % 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 (0.24), residues: 1151 helix: 2.61 (0.24), residues: 455 sheet: 0.33 (0.33), residues: 221 loop : -0.23 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 PHE 0.018 0.002 PHE R 313 TYR 0.022 0.002 TYR R 146 ARG 0.003 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 138 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.902 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 133 average time/residue: 1.6132 time to fit residues: 226.7220 Evaluate side-chains 123 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2249 time to fit residues: 1.7282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 266 HIS N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9112 Z= 0.287 Angle : 0.598 6.289 12339 Z= 0.336 Chirality : 0.044 0.144 1387 Planarity : 0.004 0.042 1589 Dihedral : 5.000 25.123 1266 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.20 % Allowed : 15.07 % Favored : 82.73 % 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: 1.25 (0.24), residues: 1151 helix: 2.25 (0.23), residues: 461 sheet: 0.30 (0.34), residues: 213 loop : -0.29 (0.27), residues: 477 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 0.025 0.002 TYR A 339 ARG 0.005 0.001 ARG R 339 *********************** 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 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.115 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 1.5988 time to fit residues: 221.1890 Evaluate side-chains 128 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.1739 time to fit residues: 3.9049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 266 HIS B 340 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9112 Z= 0.189 Angle : 0.520 5.704 12339 Z= 0.294 Chirality : 0.042 0.144 1387 Planarity : 0.004 0.041 1589 Dihedral : 4.700 23.034 1266 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.98 % Allowed : 15.62 % 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: 1.50 (0.25), residues: 1151 helix: 2.63 (0.24), residues: 455 sheet: 0.37 (0.34), residues: 211 loop : -0.29 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 PHE 0.018 0.002 PHE R 313 TYR 0.022 0.002 TYR R 146 ARG 0.004 0.000 ARG B 197 *********************** 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 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.081 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 1.5715 time to fit residues: 222.3242 Evaluate side-chains 131 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2119 time to fit residues: 1.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 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 266 HIS N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9112 Z= 0.176 Angle : 0.509 5.654 12339 Z= 0.287 Chirality : 0.041 0.144 1387 Planarity : 0.003 0.041 1589 Dihedral : 4.577 22.052 1266 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 15.84 % 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: 1.59 (0.25), residues: 1151 helix: 2.81 (0.24), residues: 449 sheet: 0.34 (0.34), residues: 211 loop : -0.27 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.017 0.002 PHE R 313 TYR 0.022 0.002 TYR R 146 ARG 0.004 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 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.054 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 1.6009 time to fit residues: 217.3449 Evaluate side-chains 125 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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 266 HIS N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116017 restraints weight = 8060.102| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.41 r_work: 0.3140 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9112 Z= 0.228 Angle : 0.554 5.847 12339 Z= 0.311 Chirality : 0.043 0.143 1387 Planarity : 0.004 0.042 1589 Dihedral : 4.773 23.793 1266 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.54 % Allowed : 16.06 % 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: 1.42 (0.24), residues: 1151 helix: 2.54 (0.24), residues: 455 sheet: 0.32 (0.34), residues: 211 loop : -0.31 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.020 0.002 PHE R 313 TYR 0.022 0.002 TYR A 339 ARG 0.005 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4264.45 seconds wall clock time: 76 minutes 11.02 seconds (4571.02 seconds total)