Starting phenix.real_space_refine on Wed Feb 14 07:41:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4f_31449/02_2024/7f4f_31449_updated.pdb" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 59 5.16 5 C 5647 2.51 5 N 1537 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 7 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2079 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1916 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 423 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2583 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 108 Classifications: {'peptide': 12} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.58 Number of scatterers: 8881 At special positions: 0 Unit cell: (113.905, 99.275, 115.995, 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) Ca 1 19.99 S 59 16.00 O 1637 8.00 N 1537 7.00 C 5647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " 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: 3.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 7 " Number of C-beta restraints generated: 2134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 36.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'R' and resid 42 through 65 Processing helix chain 'R' and resid 72 through 103 Processing helix chain 'R' and resid 110 through 147 Processing helix chain 'R' and resid 149 through 155 removed outlier: 5.072A pdb=" N HIS R 153 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 181 Processing helix chain 'R' and resid 186 through 225 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 271 through 298 removed outlier: 3.793A pdb=" N ASN R 279 " --> pdb=" O CYS R 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'A' and resid 14 through 39 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.524A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 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 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.624A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing sheet with id= A, first strand: chain 'S' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.881A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.458A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= E, first strand: chain 'A' and resid 287 through 292 removed outlier: 6.957A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.845A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.850A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.872A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.646A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.003A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.723A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.782A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1224 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: 2.59 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1442 1.31 - 1.44: 2475 1.44 - 1.57: 5054 1.57 - 1.71: 6 1.71 - 1.84: 83 Bond restraints: 9060 Sorted by residual: bond pdb=" C ALA A 269 " pdb=" O ALA A 269 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.40e+00 bond pdb=" C NLE F 4 " pdb=" O NLE F 4 " ideal model delta sigma weight residual 1.231 1.172 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CA ILE A 288 " pdb=" CB ILE A 288 " ideal model delta sigma weight residual 1.527 1.490 0.036 1.31e-02 5.83e+03 7.76e+00 bond pdb=" CA ALA A 269 " pdb=" CB ALA A 269 " ideal model delta sigma weight residual 1.528 1.570 -0.042 1.56e-02 4.11e+03 7.14e+00 bond pdb=" CD GLN R 219 " pdb=" OE1 GLN R 219 " ideal model delta sigma weight residual 1.231 1.181 0.050 1.90e-02 2.77e+03 7.00e+00 ... (remaining 9055 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.54: 145 105.54 - 112.62: 4598 112.62 - 119.71: 3223 119.71 - 126.80: 4201 126.80 - 133.89: 111 Bond angle restraints: 12278 Sorted by residual: angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 115.43 120.64 -5.21 1.41e+00 5.03e-01 1.37e+01 angle pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta sigma weight residual 121.32 113.58 7.74 2.10e+00 2.27e-01 1.36e+01 angle pdb=" N LEU R 206 " pdb=" CA LEU R 206 " pdb=" C LEU R 206 " ideal model delta sigma weight residual 110.97 114.92 -3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA TYR S 190 " pdb=" CB TYR S 190 " pdb=" CG TYR S 190 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ARG R 109 " pdb=" N ALA R 110 " pdb=" CA ALA R 110 " ideal model delta sigma weight residual 120.28 124.62 -4.34 1.34e+00 5.57e-01 1.05e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4965 17.02 - 34.05: 351 34.05 - 51.07: 44 51.07 - 68.09: 13 68.09 - 85.12: 8 Dihedral angle restraints: 5381 sinusoidal: 2077 harmonic: 3304 Sorted by residual: dihedral pdb=" CA PRO S 236 " pdb=" C PRO S 236 " pdb=" N LEU S 237 " pdb=" CA LEU S 237 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 5378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 968 0.062 - 0.124: 367 0.124 - 0.186: 58 0.186 - 0.248: 7 0.248 - 0.310: 7 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1404 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.042 2.00e-02 2.50e+03 8.45e-02 7.14e+01 pdb=" C ASN B 340 " 0.146 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.056 2.00e-02 2.50e+03 pdb=" N GLY B 341 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 191 " -0.373 9.50e-02 1.11e+02 1.71e-01 3.34e+01 pdb=" NE ARG S 191 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG S 191 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG S 191 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG S 191 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 67 " 0.254 9.50e-02 1.11e+02 1.16e-01 1.37e+01 pdb=" NE ARG S 67 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG S 67 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG S 67 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG S 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 353 2.71 - 3.26: 9339 3.26 - 3.81: 15144 3.81 - 4.35: 19989 4.35 - 4.90: 33095 Nonbonded interactions: 77920 Sorted by model distance: nonbonded pdb=" OH TYR S 175 " pdb=" OE2 GLU A 15 " model vdw 2.164 2.440 nonbonded pdb=" O LEU R 259 " pdb=" OG1 THR R 262 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP A 295 " pdb=" N LEU A 296 " model vdw 2.233 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASN R 118 " pdb=" NH2 ARG F 8 " model vdw 2.270 2.520 ... (remaining 77915 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.290 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.710 Find NCS groups from input model: 0.290 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:18.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.010 0.069 9060 Z= 0.630 Angle : 1.093 10.799 12278 Z= 0.635 Chirality : 0.064 0.310 1407 Planarity : 0.012 0.171 1555 Dihedral : 12.595 85.116 3241 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.89 (0.24), residues: 1115 helix: -0.45 (0.22), residues: 411 sheet: -0.46 (0.30), residues: 296 loop : -0.57 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.007 TRP B 339 HIS 0.020 0.004 HIS A 387 PHE 0.025 0.005 PHE R 300 TYR 0.039 0.007 TYR B 105 ARG 0.070 0.006 ARG S 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7960 (mt0) cc_final: 0.7737 (mt0) REVERT: A 271 ASN cc_start: 0.7834 (m110) cc_final: 0.7589 (m110) REVERT: A 339 TYR cc_start: 0.7520 (m-80) cc_final: 0.6882 (m-80) REVERT: B 264 TYR cc_start: 0.8710 (m-80) cc_final: 0.8493 (m-80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 1.4302 time to fit residues: 343.7355 Evaluate side-chains 149 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN S 183 GLN R 68 ASN R 91 ASN R 270 HIS A 239 ASN A 294 GLN A 371 ASN B 91 HIS B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9060 Z= 0.204 Angle : 0.637 9.244 12278 Z= 0.335 Chirality : 0.043 0.194 1407 Planarity : 0.005 0.052 1555 Dihedral : 5.919 56.580 1243 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.19 % Allowed : 11.38 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.53 (0.26), residues: 1115 helix: 1.34 (0.25), residues: 416 sheet: -0.47 (0.31), residues: 269 loop : 0.10 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.006 0.001 HIS A 362 PHE 0.016 0.002 PHE R 147 TYR 0.013 0.002 TYR S 235 ARG 0.009 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 294 ASP cc_start: 0.6702 (m-30) cc_final: 0.6223 (m-30) REVERT: B 10 GLU cc_start: 0.7810 (tp30) cc_final: 0.6973 (tp30) REVERT: B 145 TYR cc_start: 0.8775 (p90) cc_final: 0.8384 (p90) REVERT: B 266 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7391 (t70) outliers start: 21 outliers final: 7 residues processed: 173 average time/residue: 1.3532 time to fit residues: 248.1348 Evaluate side-chains 158 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 overall best weight: 2.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 142 GLN R 91 ASN ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 294 GLN A 390 GLN B 175 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9060 Z= 0.374 Angle : 0.646 9.649 12278 Z= 0.339 Chirality : 0.045 0.180 1407 Planarity : 0.005 0.052 1555 Dihedral : 5.605 53.195 1243 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 13.47 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.72 (0.26), residues: 1115 helix: 1.62 (0.25), residues: 405 sheet: -0.57 (0.30), residues: 275 loop : 0.29 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.024 0.002 PHE R 147 TYR 0.026 0.002 TYR S 190 ARG 0.005 0.001 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7331 (t0) cc_final: 0.5869 (t0) REVERT: R 114 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 264 TYR cc_start: 0.8795 (m-80) cc_final: 0.8566 (m-80) outliers start: 26 outliers final: 6 residues processed: 157 average time/residue: 1.4763 time to fit residues: 245.1310 Evaluate side-chains 141 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 114 GLN Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 267 GLN A 278 ASN B 175 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9060 Z= 0.183 Angle : 0.584 9.902 12278 Z= 0.303 Chirality : 0.042 0.177 1407 Planarity : 0.004 0.053 1555 Dihedral : 5.260 56.067 1243 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.30 % Allowed : 15.14 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.89 (0.26), residues: 1115 helix: 1.77 (0.25), residues: 411 sheet: -0.42 (0.30), residues: 274 loop : 0.30 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 301 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR S 190 ARG 0.005 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 244 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8138 (ttmm) REVERT: B 10 GLU cc_start: 0.7846 (tp30) cc_final: 0.7561 (tp30) REVERT: B 59 TYR cc_start: 0.7539 (m-80) cc_final: 0.7328 (m-80) REVERT: B 145 TYR cc_start: 0.8671 (p90) cc_final: 0.8284 (p90) REVERT: B 266 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7438 (t70) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.4362 time to fit residues: 241.6517 Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN R 270 HIS A 236 GLN A 390 GLN B 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9060 Z= 0.188 Angle : 0.559 6.976 12278 Z= 0.291 Chirality : 0.041 0.166 1407 Planarity : 0.004 0.054 1555 Dihedral : 5.095 58.073 1243 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.92 % Allowed : 15.97 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.12 (0.26), residues: 1115 helix: 2.04 (0.25), residues: 409 sheet: -0.20 (0.31), residues: 266 loop : 0.25 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 301 PHE 0.012 0.001 PHE R 147 TYR 0.018 0.001 TYR A 318 ARG 0.005 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7625 (ptpp) REVERT: B 145 TYR cc_start: 0.8713 (p90) cc_final: 0.8358 (p90) REVERT: B 266 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7453 (t70) outliers start: 28 outliers final: 9 residues processed: 158 average time/residue: 1.4307 time to fit residues: 239.2884 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS A 236 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9060 Z= 0.229 Angle : 0.584 6.765 12278 Z= 0.301 Chirality : 0.041 0.163 1407 Planarity : 0.004 0.053 1555 Dihedral : 5.054 59.368 1243 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 17.01 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.19 (0.26), residues: 1115 helix: 2.18 (0.25), residues: 409 sheet: -0.24 (0.31), residues: 266 loop : 0.25 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE R 147 TYR 0.018 0.001 TYR S 190 ARG 0.006 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8257 (tp30) cc_final: 0.7731 (tp30) REVERT: B 145 TYR cc_start: 0.8788 (p90) cc_final: 0.8434 (p90) REVERT: B 266 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7515 (t70) outliers start: 26 outliers final: 9 residues processed: 152 average time/residue: 1.4049 time to fit residues: 226.3026 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN R 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9060 Z= 0.228 Angle : 0.583 8.424 12278 Z= 0.300 Chirality : 0.042 0.168 1407 Planarity : 0.004 0.052 1555 Dihedral : 5.003 59.702 1243 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.30 % Allowed : 17.95 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1115 helix: 2.25 (0.25), residues: 409 sheet: -0.24 (0.31), residues: 266 loop : 0.31 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 PHE 0.012 0.001 PHE R 147 TYR 0.019 0.001 TYR S 190 ARG 0.007 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7157 (t70) cc_final: 0.6612 (t70) REVERT: B 266 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (t70) outliers start: 22 outliers final: 8 residues processed: 143 average time/residue: 1.4118 time to fit residues: 214.3938 Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS A 390 GLN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9060 Z= 0.283 Angle : 0.622 8.116 12278 Z= 0.318 Chirality : 0.042 0.169 1407 Planarity : 0.004 0.051 1555 Dihedral : 5.022 56.518 1243 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.77 % Allowed : 18.79 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.20 (0.26), residues: 1115 helix: 2.25 (0.25), residues: 409 sheet: -0.32 (0.31), residues: 267 loop : 0.26 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 PHE 0.014 0.001 PHE R 147 TYR 0.020 0.002 TYR S 190 ARG 0.011 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 145 TYR cc_start: 0.8742 (p90) cc_final: 0.8366 (p90) REVERT: B 266 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7738 (t70) outliers start: 17 outliers final: 6 residues processed: 149 average time/residue: 1.4537 time to fit residues: 229.4152 Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS A 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9060 Z= 0.193 Angle : 0.584 9.115 12278 Z= 0.301 Chirality : 0.041 0.161 1407 Planarity : 0.004 0.052 1555 Dihedral : 4.911 57.758 1243 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.67 % Allowed : 20.04 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1115 helix: 2.26 (0.25), residues: 409 sheet: -0.32 (0.30), residues: 270 loop : 0.30 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 PHE 0.010 0.001 PHE R 147 TYR 0.021 0.001 TYR A 318 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.6803 (t70) cc_final: 0.6364 (t70) REVERT: R 115 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7594 (tp40) REVERT: B 145 TYR cc_start: 0.8603 (p90) cc_final: 0.8283 (p90) REVERT: B 266 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7715 (t70) outliers start: 16 outliers final: 8 residues processed: 145 average time/residue: 1.3782 time to fit residues: 212.1967 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9060 Z= 0.242 Angle : 0.625 10.278 12278 Z= 0.319 Chirality : 0.042 0.164 1407 Planarity : 0.004 0.051 1555 Dihedral : 4.914 53.258 1243 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.15 % Allowed : 20.56 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1115 helix: 2.29 (0.25), residues: 403 sheet: -0.33 (0.30), residues: 277 loop : 0.38 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS R 270 PHE 0.012 0.001 PHE R 147 TYR 0.022 0.002 TYR A 318 ARG 0.008 0.000 ARG S 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 115 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7598 (tp40) REVERT: B 145 TYR cc_start: 0.8670 (p90) cc_final: 0.8296 (p90) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 1.4490 time to fit residues: 224.2157 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.0570 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.066776 restraints weight = 16988.524| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.79 r_work: 0.2784 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9060 Z= 0.379 Angle : 0.675 8.954 12278 Z= 0.345 Chirality : 0.044 0.183 1407 Planarity : 0.004 0.050 1555 Dihedral : 5.252 58.186 1243 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.25 % Allowed : 21.29 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.26), residues: 1115 helix: 2.09 (0.25), residues: 404 sheet: -0.48 (0.30), residues: 277 loop : 0.20 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 169 HIS 0.010 0.001 HIS R 270 PHE 0.017 0.002 PHE R 147 TYR 0.024 0.002 TYR A 318 ARG 0.007 0.000 ARG S 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4073.60 seconds wall clock time: 73 minutes 19.75 seconds (4399.75 seconds total)