Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 15:01:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/04_2023/7ckw_30392_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 5158 2.51 5 N 1403 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8103 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2202 Unusual residues: {'CLR': 1, 'G3C': 1} Classifications: {'peptide': 273, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 263, None: 2} Not linked: pdbres="LEU R 344 " pdbres="G3C R 501 " Not linked: pdbres="G3C R 501 " pdbres="CLR R 502 " Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.80, per 1000 atoms: 0.59 Number of scatterers: 8103 At special positions: 0 Unit cell: (89, 87, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 53 16.00 O 1488 8.00 N 1403 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 37.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.709A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 255 through 277 removed outlier: 5.938A pdb=" N LEU A 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.961A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.604A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.651A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 23 through 49 Processing helix chain 'R' and resid 58 through 76 removed outlier: 4.269A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 85 Processing helix chain 'R' and resid 93 through 125 removed outlier: 5.183A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.108A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.904A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 236 removed outlier: 3.849A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 277 removed outlier: 3.576A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 294 Proline residue: R 287 - end of helix removed outlier: 4.076A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 330 removed outlier: 4.058A pdb=" N ASP R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 343 removed outlier: 3.781A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.004A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.747A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.744A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= E, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.797A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.479A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.007A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.782A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.653A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 927 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: 2.30 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2630 1.34 - 1.46: 1961 1.46 - 1.58: 3610 1.58 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8274 Sorted by residual: bond pdb=" C02 G3C R 501 " pdb=" O01 G3C R 501 " ideal model delta sigma weight residual 1.345 1.399 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C11 G3C R 501 " pdb=" O12 G3C R 501 " ideal model delta sigma weight residual 1.349 1.402 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" N HIS A 357 " pdb=" CA HIS A 357 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 7.01e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" C03 G3C R 501 " pdb=" O04 G3C R 501 " ideal model delta sigma weight residual 1.352 1.400 -0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 188 106.89 - 113.68: 4570 113.68 - 120.48: 3246 120.48 - 127.27: 3137 127.27 - 134.06: 87 Bond angle restraints: 11228 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.14e+00 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 113.42 111.12 2.30 1.17e+00 7.31e-01 3.86e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" N LEU R 76 " ideal model delta sigma weight residual 118.90 117.20 1.70 9.40e-01 1.13e+00 3.28e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" O VAL R 75 " ideal model delta sigma weight residual 118.90 120.45 -1.55 8.80e-01 1.29e+00 3.11e+00 angle pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 122.90 120.65 2.25 1.28e+00 6.10e-01 3.09e+00 ... (remaining 11223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4401 17.29 - 34.57: 390 34.57 - 51.86: 87 51.86 - 69.14: 13 69.14 - 86.43: 4 Dihedral angle restraints: 4895 sinusoidal: 1879 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 32.63 60.37 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.75 52.75 1 2.00e+01 2.50e-03 9.47e+00 dihedral pdb=" CB MET B 217 " pdb=" CG MET B 217 " pdb=" SD MET B 217 " pdb=" CE MET B 217 " ideal model delta sinusoidal sigma weight residual -180.00 -122.55 -57.45 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 4892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1090 0.055 - 0.109: 178 0.109 - 0.164: 10 0.164 - 0.219: 0 0.219 - 0.273: 1 Chirality restraints: 1279 Sorted by residual: chirality pdb=" C07 G3C R 501 " pdb=" C06 G3C R 501 " pdb=" C08 G3C R 501 " pdb=" C15 G3C R 501 " both_signs ideal model delta sigma weight residual False -2.44 -2.71 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1276 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 114 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LEU R 114 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU R 114 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS R 115 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 104 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ILE R 104 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 104 " -0.009 2.00e-02 2.50e+03 pdb=" N MET R 105 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO R 206 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.019 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 433 2.72 - 3.27: 8610 3.27 - 3.81: 14852 3.81 - 4.36: 18257 4.36 - 4.90: 30212 Nonbonded interactions: 72364 Sorted by model distance: nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.178 2.440 nonbonded pdb=" OG SER R 199 " pdb=" ND2 ASN R 292 " model vdw 2.179 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.186 2.440 nonbonded pdb=" CG1 VAL B 200 " pdb=" CE2 PHE B 234 " model vdw 2.200 3.760 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.222 2.440 ... (remaining 72359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.990 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 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 : 0.002 0.054 8274 Z= 0.161 Angle : 0.480 5.340 11228 Z= 0.288 Chirality : 0.039 0.273 1279 Planarity : 0.003 0.033 1418 Dihedral : 13.744 86.426 2923 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.74 % 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: -3.30 (0.23), residues: 1015 helix: -1.57 (0.22), residues: 383 sheet: -2.85 (0.32), residues: 188 loop : -2.31 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 286 average time/residue: 0.2574 time to fit residues: 93.5017 Evaluate side-chains 217 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0744 time to fit residues: 1.9641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.0040 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 371 ASN A 390 GLN B 125 ASN B 266 HIS B 340 ASN G 18 GLN N 84 ASN N 120 GLN N 123 GLN R 60 ASN R 323 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 8274 Z= 0.187 Angle : 0.518 6.854 11228 Z= 0.269 Chirality : 0.042 0.178 1279 Planarity : 0.005 0.051 1418 Dihedral : 4.087 50.395 1130 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 3.02 % 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: -2.09 (0.25), residues: 1015 helix: -0.31 (0.25), residues: 393 sheet: -2.55 (0.33), residues: 194 loop : -1.71 (0.29), residues: 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 256 average time/residue: 0.2222 time to fit residues: 75.4169 Evaluate side-chains 227 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0855 time to fit residues: 2.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 267 GLN A 390 GLN B 237 ASN N 53 GLN N 120 GLN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8274 Z= 0.243 Angle : 0.541 8.840 11228 Z= 0.278 Chirality : 0.041 0.145 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.231 50.378 1130 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1015 helix: 0.14 (0.26), residues: 392 sheet: -2.29 (0.32), residues: 208 loop : -1.40 (0.31), residues: 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 0.2103 time to fit residues: 70.3692 Evaluate side-chains 235 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1118 time to fit residues: 3.9906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 chunk 81 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN N 53 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.003 0.065 8274 Z= 0.225 Angle : 0.566 11.997 11228 Z= 0.285 Chirality : 0.042 0.204 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.349 51.477 1130 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 2.91 % 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: -1.33 (0.26), residues: 1015 helix: 0.40 (0.26), residues: 388 sheet: -2.26 (0.35), residues: 189 loop : -1.30 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 0.977 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 241 average time/residue: 0.2159 time to fit residues: 69.6987 Evaluate side-chains 234 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0856 time to fit residues: 3.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 40 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 35 ASN N 53 GLN N 84 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 8274 Z= 0.212 Angle : 0.552 9.777 11228 Z= 0.279 Chirality : 0.042 0.169 1279 Planarity : 0.004 0.039 1418 Dihedral : 4.449 53.171 1130 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.09 % 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: -1.16 (0.27), residues: 1015 helix: 0.54 (0.27), residues: 384 sheet: -2.27 (0.34), residues: 198 loop : -1.10 (0.31), residues: 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 243 average time/residue: 0.2294 time to fit residues: 73.6055 Evaluate side-chains 227 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1216 time to fit residues: 3.0253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 125 ASN G 18 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8274 Z= 0.282 Angle : 0.591 10.635 11228 Z= 0.300 Chirality : 0.043 0.189 1279 Planarity : 0.004 0.046 1418 Dihedral : 4.513 53.248 1130 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.40 % 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: -1.22 (0.26), residues: 1015 helix: 0.45 (0.26), residues: 388 sheet: -2.20 (0.34), residues: 203 loop : -1.14 (0.30), residues: 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 0.854 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 241 average time/residue: 0.2245 time to fit residues: 71.8487 Evaluate side-chains 226 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0814 time to fit residues: 2.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8274 Z= 0.231 Angle : 0.598 10.366 11228 Z= 0.299 Chirality : 0.043 0.172 1279 Planarity : 0.004 0.067 1418 Dihedral : 4.535 45.622 1130 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 1015 helix: 0.43 (0.26), residues: 384 sheet: -1.96 (0.36), residues: 199 loop : -0.98 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 235 average time/residue: 0.2204 time to fit residues: 68.6336 Evaluate side-chains 224 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0802 time to fit residues: 2.7627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8274 Z= 0.231 Angle : 0.610 11.635 11228 Z= 0.304 Chirality : 0.043 0.171 1279 Planarity : 0.004 0.043 1418 Dihedral : 4.485 42.830 1130 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.51 % 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: -1.02 (0.27), residues: 1015 helix: 0.47 (0.26), residues: 389 sheet: -1.88 (0.35), residues: 203 loop : -1.01 (0.32), residues: 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 0.893 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 224 average time/residue: 0.2117 time to fit residues: 63.6967 Evaluate side-chains 219 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0877 time to fit residues: 2.3861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0470 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8274 Z= 0.232 Angle : 0.616 10.528 11228 Z= 0.309 Chirality : 0.043 0.173 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.461 33.718 1130 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.81 % 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: -0.98 (0.27), residues: 1015 helix: 0.41 (0.26), residues: 390 sheet: -1.98 (0.36), residues: 187 loop : -0.87 (0.31), residues: 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 223 average time/residue: 0.2089 time to fit residues: 62.9161 Evaluate side-chains 217 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0764 time to fit residues: 1.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8274 Z= 0.209 Angle : 0.635 9.916 11228 Z= 0.312 Chirality : 0.043 0.170 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.442 31.333 1130 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.27), residues: 1015 helix: 0.43 (0.26), residues: 388 sheet: -1.93 (0.37), residues: 173 loop : -0.86 (0.31), residues: 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 0.888 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 220 average time/residue: 0.2272 time to fit residues: 67.1953 Evaluate side-chains 215 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0786 time to fit residues: 1.3850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.0030 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.208004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173076 restraints weight = 8827.399| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.12 r_work: 0.3834 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8274 Z= 0.201 Angle : 0.627 9.609 11228 Z= 0.309 Chirality : 0.043 0.170 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.392 28.083 1130 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.81 % 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: -0.84 (0.27), residues: 1015 helix: 0.51 (0.26), residues: 389 sheet: -1.94 (0.37), residues: 173 loop : -0.81 (0.31), residues: 453 =============================================================================== Job complete usr+sys time: 2298.36 seconds wall clock time: 42 minutes 23.94 seconds (2543.94 seconds total)