Starting phenix.real_space_refine on Mon Mar 11 15:07:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/03_2024/7ljc_23390.pdb" } resolution = 3.0 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= 0.003 sd= 0.037 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 S 55 5.16 5 Cl 3 4.86 5 C 5505 2.51 5 N 1442 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 23": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 266": "NH1" <-> "NH2" Residue "R PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2226 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1989 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 326 Unusual residues: {'CLR': 6, 'G4C': 1, 'PLM': 6, 'SK0': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Time building chain proxies: 5.14, per 1000 atoms: 0.60 Number of scatterers: 8544 At special positions: 0 Unit cell: (91.96, 108.68, 123.31, 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 3 17.00 S 55 16.00 O 1539 8.00 N 1442 7.00 C 5505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 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 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 21 through 51 Processing helix chain 'R' and resid 51 through 56 removed outlier: 4.122A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.057A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.339A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.294A 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 191 through 203 Processing helix chain 'R' and resid 203 through 240 Processing helix chain 'R' and resid 265 through 298 removed outlier: 3.696A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.975A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.500A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.621A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.985A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.829A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.618A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 5.959A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.803A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.926A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.263A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.809A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.225A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.763A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.926A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1302 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: 2.51 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2148 1.33 - 1.46: 1881 1.46 - 1.58: 4623 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8730 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.498 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.02e+00 bond pdb=" C ASN R 327 " pdb=" N PRO R 328 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.64e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.21e+00 bond pdb=" C LEU R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.18e+00 ... (remaining 8725 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.69: 158 105.69 - 112.79: 4709 112.79 - 119.89: 2876 119.89 - 126.98: 3980 126.98 - 134.08: 106 Bond angle restraints: 11829 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N GLY B 244 " pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 113.18 105.26 7.92 2.37e+00 1.78e-01 1.12e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.06 114.24 -5.18 1.70e+00 3.46e-01 9.28e+00 ... (remaining 11824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5350 17.55 - 35.09: 135 35.09 - 52.64: 34 52.64 - 70.18: 4 70.18 - 87.73: 2 Dihedral angle restraints: 5525 sinusoidal: 2489 harmonic: 3036 Sorted by residual: dihedral pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1158 0.091 - 0.183: 149 0.183 - 0.274: 12 0.274 - 0.366: 6 0.366 - 0.457: 6 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 1328 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " 0.225 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" C05 G4C R 502 " -0.051 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " 0.180 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " -0.036 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " -0.227 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 101 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ALA R 101 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA R 101 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 102 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 110 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER R 110 " -0.068 2.00e-02 2.50e+03 pdb=" O SER R 110 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 111 " 0.023 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2090 2.81 - 3.33: 7663 3.33 - 3.85: 14340 3.85 - 4.38: 16516 4.38 - 4.90: 28840 Nonbonded interactions: 69449 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.288 2.440 nonbonded pdb=" OG SER R 198 " pdb=" O02 SK0 R 501 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR R 59 " pdb=" OH TYR R 131 " model vdw 2.371 2.440 nonbonded pdb=" NH2 ARG R 133 " pdb=" O LYS A 78 " model vdw 2.371 2.520 ... (remaining 69444 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.710 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.005 0.143 8730 Z= 0.346 Angle : 1.005 9.518 11829 Z= 0.544 Chirality : 0.068 0.457 1331 Planarity : 0.009 0.156 1458 Dihedral : 9.081 87.728 3541 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % 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 (0.23), residues: 1024 helix: 0.47 (0.21), residues: 389 sheet: -0.65 (0.32), residues: 239 loop : -1.87 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 133 HIS 0.009 0.003 HIS A 209 PHE 0.030 0.003 PHE B 278 TYR 0.022 0.002 TYR N 95 ARG 0.012 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: R 76 LEU cc_start: 0.7934 (mp) cc_final: 0.7726 (mt) REVERT: R 126 SER cc_start: 0.8928 (t) cc_final: 0.8707 (p) REVERT: R 127 SER cc_start: 0.8729 (m) cc_final: 0.8474 (p) REVERT: R 154 ILE cc_start: 0.7667 (mt) cc_final: 0.7186 (tt) REVERT: R 270 VAL cc_start: 0.8186 (t) cc_final: 0.7877 (p) REVERT: A 24 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8319 (mmmt) REVERT: A 60 MET cc_start: 0.6708 (ttt) cc_final: 0.6372 (ttt) REVERT: A 75 GLN cc_start: 0.7846 (tt0) cc_final: 0.7550 (tt0) REVERT: A 142 PHE cc_start: 0.8762 (m-80) cc_final: 0.8436 (m-80) REVERT: A 169 ARG cc_start: 0.8271 (ptp-170) cc_final: 0.7917 (ptp-170) REVERT: A 202 THR cc_start: 0.8451 (m) cc_final: 0.8031 (p) REVERT: A 208 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8299 (mtm180) REVERT: A 229 ASN cc_start: 0.8659 (m-40) cc_final: 0.8265 (m-40) REVERT: A 233 ASP cc_start: 0.8578 (m-30) cc_final: 0.8363 (m-30) REVERT: A 244 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 14 LEU cc_start: 0.8487 (mt) cc_final: 0.8282 (mt) REVERT: B 25 CYS cc_start: 0.8473 (m) cc_final: 0.8115 (p) REVERT: B 52 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: B 98 SER cc_start: 0.8371 (m) cc_final: 0.7990 (p) REVERT: B 111 TYR cc_start: 0.8228 (m-80) cc_final: 0.7865 (m-80) REVERT: B 195 ASP cc_start: 0.7961 (p0) cc_final: 0.7746 (p0) REVERT: B 197 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7580 (mmt180) REVERT: B 239 ASN cc_start: 0.8115 (m-40) cc_final: 0.7770 (m-40) REVERT: B 247 ASP cc_start: 0.7841 (p0) cc_final: 0.7555 (p0) REVERT: B 254 ASP cc_start: 0.8653 (t0) cc_final: 0.8419 (t70) REVERT: B 258 ASP cc_start: 0.8091 (t0) cc_final: 0.7372 (t0) REVERT: B 262 MET cc_start: 0.8576 (ttm) cc_final: 0.8308 (ttm) REVERT: B 264 TYR cc_start: 0.8593 (m-80) cc_final: 0.8101 (m-80) REVERT: B 273 ILE cc_start: 0.8118 (mt) cc_final: 0.7872 (mt) REVERT: B 289 TYR cc_start: 0.8516 (m-80) cc_final: 0.8243 (m-80) REVERT: B 312 ASP cc_start: 0.8630 (t0) cc_final: 0.8362 (t0) REVERT: N 112 SER cc_start: 0.8084 (p) cc_final: 0.7721 (m) outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 1.0466 time to fit residues: 329.3247 Evaluate side-chains 256 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.0030 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 164 HIS R 222 GLN A 19 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 62 HIS B 88 ASN B 91 HIS B 259 GLN N 5 GLN N 74 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8730 Z= 0.230 Angle : 0.557 14.853 11829 Z= 0.288 Chirality : 0.041 0.195 1331 Planarity : 0.005 0.048 1458 Dihedral : 7.623 89.099 1650 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.02 % Allowed : 10.95 % Favored : 86.03 % 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: 0.48 (0.25), residues: 1024 helix: 2.32 (0.23), residues: 407 sheet: -0.49 (0.34), residues: 212 loop : -1.35 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.009 0.001 HIS A 82 PHE 0.020 0.002 PHE B 199 TYR 0.013 0.002 TYR B 59 ARG 0.008 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: R 159 VAL cc_start: 0.8421 (t) cc_final: 0.8132 (m) REVERT: R 270 VAL cc_start: 0.8168 (t) cc_final: 0.7907 (p) REVERT: R 331 TYR cc_start: 0.8131 (m-80) cc_final: 0.7820 (m-80) REVERT: A 24 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8430 (tppp) REVERT: A 27 GLU cc_start: 0.8238 (tp30) cc_final: 0.8027 (tp30) REVERT: A 60 MET cc_start: 0.6542 (ttt) cc_final: 0.6207 (ttt) REVERT: A 75 GLN cc_start: 0.7674 (tt0) cc_final: 0.7299 (tt0) REVERT: A 89 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8329 (mt0) REVERT: A 142 PHE cc_start: 0.8769 (m-80) cc_final: 0.8466 (m-80) REVERT: A 170 TYR cc_start: 0.8466 (t80) cc_final: 0.8095 (t80) REVERT: A 202 THR cc_start: 0.8282 (m) cc_final: 0.7942 (p) REVERT: A 208 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8374 (mtm180) REVERT: A 229 ASN cc_start: 0.8812 (m-40) cc_final: 0.8443 (m-40) REVERT: A 233 ASP cc_start: 0.8580 (m-30) cc_final: 0.8372 (m-30) REVERT: A 244 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 70 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8346 (pt) REVERT: B 98 SER cc_start: 0.8448 (m) cc_final: 0.8053 (p) REVERT: B 110 ASN cc_start: 0.7906 (m-40) cc_final: 0.7430 (m110) REVERT: B 114 CYS cc_start: 0.8517 (p) cc_final: 0.8272 (p) REVERT: B 125 ASN cc_start: 0.8671 (t0) cc_final: 0.8445 (m-40) REVERT: B 158 VAL cc_start: 0.8000 (t) cc_final: 0.7718 (p) REVERT: B 221 THR cc_start: 0.8627 (m) cc_final: 0.8348 (t) REVERT: B 226 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 239 ASN cc_start: 0.8208 (m-40) cc_final: 0.7931 (m-40) REVERT: B 254 ASP cc_start: 0.8719 (t0) cc_final: 0.8490 (t70) REVERT: B 256 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8129 (mtt90) REVERT: B 258 ASP cc_start: 0.8204 (t0) cc_final: 0.7876 (t0) REVERT: B 289 TYR cc_start: 0.8738 (m-80) cc_final: 0.8480 (m-80) REVERT: B 312 ASP cc_start: 0.8658 (t0) cc_final: 0.8342 (t0) REVERT: N 112 SER cc_start: 0.8364 (p) cc_final: 0.8122 (m) outliers start: 27 outliers final: 10 residues processed: 277 average time/residue: 1.1343 time to fit residues: 335.1082 Evaluate side-chains 254 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 5 GLN 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: 0.7980 chunk 76 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 99 optimal weight: 0.2980 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 75 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 88 ASN B 230 ASN B 259 GLN B 295 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8730 Z= 0.172 Angle : 0.533 16.431 11829 Z= 0.269 Chirality : 0.040 0.136 1331 Planarity : 0.004 0.045 1458 Dihedral : 7.041 86.884 1648 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.79 % Allowed : 13.52 % Favored : 83.69 % 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: 0.94 (0.26), residues: 1024 helix: 2.74 (0.24), residues: 411 sheet: -0.38 (0.35), residues: 189 loop : -1.07 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 133 HIS 0.006 0.001 HIS A 82 PHE 0.018 0.001 PHE B 199 TYR 0.013 0.001 TYR N 117 ARG 0.009 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 154 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7263 (tt) REVERT: R 159 VAL cc_start: 0.8413 (t) cc_final: 0.8133 (m) REVERT: R 162 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7923 (p) REVERT: R 270 VAL cc_start: 0.8156 (t) cc_final: 0.7874 (p) REVERT: A 27 GLU cc_start: 0.8198 (tp30) cc_final: 0.7982 (tp30) REVERT: A 142 PHE cc_start: 0.8740 (m-80) cc_final: 0.8425 (m-80) REVERT: A 169 ARG cc_start: 0.8439 (ptp-170) cc_final: 0.8150 (mtm110) REVERT: A 170 TYR cc_start: 0.8475 (t80) cc_final: 0.8114 (t80) REVERT: A 199 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: A 202 THR cc_start: 0.8226 (m) cc_final: 0.7877 (p) REVERT: A 208 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8383 (mtm180) REVERT: A 229 ASN cc_start: 0.8813 (m-40) cc_final: 0.8449 (m-40) REVERT: A 241 ARG cc_start: 0.8453 (mtp-110) cc_final: 0.8248 (ttp80) REVERT: A 244 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8311 (mt-10) REVERT: B 25 CYS cc_start: 0.8523 (m) cc_final: 0.7962 (p) REVERT: B 70 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8251 (OUTLIER) REVERT: B 98 SER cc_start: 0.8370 (m) cc_final: 0.7984 (p) REVERT: B 105 TYR cc_start: 0.8770 (t80) cc_final: 0.8316 (t80) REVERT: B 110 ASN cc_start: 0.8041 (m-40) cc_final: 0.7807 (m110) REVERT: B 124 TYR cc_start: 0.8651 (m-80) cc_final: 0.8206 (m-80) REVERT: B 197 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7860 (mtt180) REVERT: B 221 THR cc_start: 0.8595 (m) cc_final: 0.8304 (t) REVERT: B 226 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8528 (mt-10) REVERT: B 239 ASN cc_start: 0.8104 (m-40) cc_final: 0.7809 (m-40) REVERT: B 245 SER cc_start: 0.8656 (m) cc_final: 0.8339 (t) REVERT: B 256 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8109 (mtt90) REVERT: B 258 ASP cc_start: 0.8294 (t0) cc_final: 0.7913 (t0) REVERT: B 259 GLN cc_start: 0.8619 (pt0) cc_final: 0.8411 (pt0) REVERT: B 312 ASP cc_start: 0.8626 (t0) cc_final: 0.8314 (t0) outliers start: 25 outliers final: 16 residues processed: 251 average time/residue: 1.0732 time to fit residues: 287.7888 Evaluate side-chains 248 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 75 GLN A 123 ASN A 130 ASN A 236 GLN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8730 Z= 0.220 Angle : 0.522 15.347 11829 Z= 0.267 Chirality : 0.040 0.139 1331 Planarity : 0.004 0.054 1458 Dihedral : 6.624 86.720 1646 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.57 % Allowed : 15.53 % Favored : 81.90 % 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: 0.97 (0.26), residues: 1024 helix: 2.67 (0.24), residues: 416 sheet: -0.54 (0.33), residues: 198 loop : -0.90 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 133 HIS 0.006 0.001 HIS A 209 PHE 0.017 0.001 PHE B 199 TYR 0.016 0.002 TYR N 117 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: R 159 VAL cc_start: 0.8364 (t) cc_final: 0.8078 (m) REVERT: R 162 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8038 (p) REVERT: R 196 ILE cc_start: 0.8705 (mm) cc_final: 0.8483 (mp) REVERT: R 270 VAL cc_start: 0.8195 (t) cc_final: 0.7913 (p) REVERT: A 60 MET cc_start: 0.6385 (ttt) cc_final: 0.6058 (ttt) REVERT: A 114 ASP cc_start: 0.8215 (m-30) cc_final: 0.7636 (m-30) REVERT: A 142 PHE cc_start: 0.8735 (m-80) cc_final: 0.8457 (m-80) REVERT: A 146 GLN cc_start: 0.8551 (mm110) cc_final: 0.8181 (mm-40) REVERT: A 170 TYR cc_start: 0.8514 (t80) cc_final: 0.8164 (t80) REVERT: A 202 THR cc_start: 0.8213 (m) cc_final: 0.7913 (p) REVERT: A 208 ARG cc_start: 0.8656 (mtm180) cc_final: 0.8437 (mtm180) REVERT: A 229 ASN cc_start: 0.8665 (m-40) cc_final: 0.8449 (m-40) REVERT: A 244 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8379 (mt-10) REVERT: B 98 SER cc_start: 0.8439 (m) cc_final: 0.8072 (p) REVERT: B 160 SER cc_start: 0.8331 (t) cc_final: 0.8013 (p) REVERT: B 197 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (mtt180) REVERT: B 221 THR cc_start: 0.8660 (m) cc_final: 0.8389 (t) REVERT: B 226 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 239 ASN cc_start: 0.8255 (m-40) cc_final: 0.8005 (m-40) REVERT: B 245 SER cc_start: 0.8761 (m) cc_final: 0.8545 (p) REVERT: B 254 ASP cc_start: 0.8671 (t0) cc_final: 0.8405 (t70) REVERT: B 256 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8202 (mtt90) REVERT: B 258 ASP cc_start: 0.8405 (t0) cc_final: 0.8113 (t0) REVERT: B 312 ASP cc_start: 0.8632 (t0) cc_final: 0.8292 (t0) outliers start: 23 outliers final: 14 residues processed: 255 average time/residue: 1.1932 time to fit residues: 323.2475 Evaluate side-chains 262 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 236 GLN B 88 ASN B 110 ASN B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8730 Z= 0.216 Angle : 0.525 16.290 11829 Z= 0.266 Chirality : 0.040 0.133 1331 Planarity : 0.004 0.055 1458 Dihedral : 6.368 86.004 1646 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.02 % Allowed : 16.31 % Favored : 80.67 % 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: 1.09 (0.26), residues: 1024 helix: 2.76 (0.24), residues: 412 sheet: -0.47 (0.33), residues: 214 loop : -0.79 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 133 HIS 0.005 0.001 HIS A 209 PHE 0.023 0.001 PHE R 333 TYR 0.017 0.002 TYR N 117 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8478 (mtt) REVERT: R 159 VAL cc_start: 0.8384 (t) cc_final: 0.8107 (m) REVERT: R 162 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8072 (p) REVERT: R 196 ILE cc_start: 0.8762 (mm) cc_final: 0.8557 (mp) REVERT: R 215 THR cc_start: 0.8940 (m) cc_final: 0.8650 (p) REVERT: R 270 VAL cc_start: 0.8207 (t) cc_final: 0.7920 (p) REVERT: A 60 MET cc_start: 0.6334 (ttt) cc_final: 0.6014 (ttt) REVERT: A 114 ASP cc_start: 0.8203 (m-30) cc_final: 0.7651 (m-30) REVERT: A 131 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: A 146 GLN cc_start: 0.8518 (mm110) cc_final: 0.8222 (mm-40) REVERT: A 169 ARG cc_start: 0.8392 (ptp-170) cc_final: 0.8147 (mtm110) REVERT: A 170 TYR cc_start: 0.8518 (t80) cc_final: 0.8133 (t80) REVERT: A 199 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8156 (ttp-170) REVERT: A 202 THR cc_start: 0.8198 (m) cc_final: 0.7898 (p) REVERT: A 208 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8424 (mtm180) REVERT: A 244 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 25 CYS cc_start: 0.8577 (m) cc_final: 0.7919 (p) REVERT: B 48 ARG cc_start: 0.8569 (mmt180) cc_final: 0.8368 (mmt-90) REVERT: B 98 SER cc_start: 0.8453 (m) cc_final: 0.8103 (p) REVERT: B 160 SER cc_start: 0.8323 (t) cc_final: 0.8034 (p) REVERT: B 197 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7885 (mtt180) REVERT: B 239 ASN cc_start: 0.8299 (m-40) cc_final: 0.7920 (m110) REVERT: B 245 SER cc_start: 0.8746 (m) cc_final: 0.8544 (p) REVERT: B 254 ASP cc_start: 0.8662 (t0) cc_final: 0.8391 (t70) REVERT: B 256 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8123 (mtt90) REVERT: B 312 ASP cc_start: 0.8635 (t0) cc_final: 0.8315 (t0) REVERT: N 25 SER cc_start: 0.8119 (t) cc_final: 0.7759 (m) REVERT: N 29 PHE cc_start: 0.8502 (t80) cc_final: 0.8189 (t80) outliers start: 27 outliers final: 13 residues processed: 248 average time/residue: 1.0957 time to fit residues: 290.0513 Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 238 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 229 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8730 Z= 0.291 Angle : 0.567 19.335 11829 Z= 0.284 Chirality : 0.041 0.138 1331 Planarity : 0.004 0.064 1458 Dihedral : 6.283 86.455 1646 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 17.32 % Favored : 80.22 % 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 (0.26), residues: 1024 helix: 2.54 (0.24), residues: 417 sheet: -0.61 (0.33), residues: 216 loop : -0.67 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 133 HIS 0.007 0.001 HIS A 209 PHE 0.014 0.002 PHE B 199 TYR 0.019 0.002 TYR N 117 ARG 0.010 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: R 162 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8215 (p) REVERT: R 270 VAL cc_start: 0.8256 (t) cc_final: 0.7967 (p) REVERT: R 333 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8096 (t80) REVERT: A 60 MET cc_start: 0.6345 (ttt) cc_final: 0.6024 (ttt) REVERT: A 93 ARG cc_start: 0.8831 (ptt90) cc_final: 0.8496 (ptt180) REVERT: A 114 ASP cc_start: 0.8192 (m-30) cc_final: 0.7666 (m-30) REVERT: A 152 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8664 (ttmt) REVERT: A 170 TYR cc_start: 0.8546 (t80) cc_final: 0.8149 (t80) REVERT: A 199 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8172 (ttp-170) REVERT: A 202 THR cc_start: 0.8228 (m) cc_final: 0.7941 (p) REVERT: A 208 ARG cc_start: 0.8679 (mtm180) cc_final: 0.8478 (mtm180) REVERT: A 225 ARG cc_start: 0.8158 (tpp-160) cc_final: 0.7937 (tpp-160) REVERT: B 25 CYS cc_start: 0.8588 (m) cc_final: 0.7916 (p) REVERT: B 48 ARG cc_start: 0.8651 (mmt180) cc_final: 0.8413 (mmt-90) REVERT: B 160 SER cc_start: 0.8290 (t) cc_final: 0.8041 (p) REVERT: B 197 ARG cc_start: 0.8129 (mmt180) cc_final: 0.7866 (mtt180) REVERT: B 230 ASN cc_start: 0.8430 (m-40) cc_final: 0.8030 (m-40) REVERT: B 239 ASN cc_start: 0.8346 (m-40) cc_final: 0.7908 (m110) REVERT: B 256 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8115 (mtt90) REVERT: B 312 ASP cc_start: 0.8663 (t0) cc_final: 0.8325 (t0) REVERT: N 25 SER cc_start: 0.8246 (t) cc_final: 0.7844 (m) outliers start: 22 outliers final: 12 residues processed: 239 average time/residue: 1.1629 time to fit residues: 295.6353 Evaluate side-chains 248 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 75 GLN B 88 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8730 Z= 0.172 Angle : 0.539 19.942 11829 Z= 0.266 Chirality : 0.039 0.135 1331 Planarity : 0.004 0.055 1458 Dihedral : 6.056 84.345 1646 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 18.77 % Favored : 78.88 % 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: 1.10 (0.26), residues: 1024 helix: 2.78 (0.24), residues: 415 sheet: -0.73 (0.33), residues: 218 loop : -0.63 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.014 0.001 PHE B 199 TYR 0.016 0.001 TYR N 117 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: R 162 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8077 (p) REVERT: R 270 VAL cc_start: 0.8210 (t) cc_final: 0.7918 (p) REVERT: R 333 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8121 (t80) REVERT: R 338 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7455 (mtt180) REVERT: A 60 MET cc_start: 0.6329 (ttt) cc_final: 0.6009 (ttt) REVERT: A 146 GLN cc_start: 0.8546 (mm110) cc_final: 0.8297 (mm-40) REVERT: A 170 TYR cc_start: 0.8514 (t80) cc_final: 0.8166 (t80) REVERT: A 199 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8088 (ttp-170) REVERT: A 202 THR cc_start: 0.8100 (m) cc_final: 0.7807 (p) REVERT: A 225 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7955 (tpp-160) REVERT: A 244 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 25 CYS cc_start: 0.8571 (m) cc_final: 0.7922 (p) REVERT: B 160 SER cc_start: 0.8077 (t) cc_final: 0.7790 (p) REVERT: B 197 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7825 (mtt180) REVERT: B 230 ASN cc_start: 0.8452 (m-40) cc_final: 0.8047 (m-40) REVERT: B 239 ASN cc_start: 0.8334 (m-40) cc_final: 0.7939 (m110) REVERT: N 25 SER cc_start: 0.8163 (t) cc_final: 0.7844 (m) REVERT: N 29 PHE cc_start: 0.8333 (t80) cc_final: 0.8047 (t80) outliers start: 21 outliers final: 11 residues processed: 235 average time/residue: 1.2244 time to fit residues: 305.8586 Evaluate side-chains 243 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 229 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 75 GLN B 88 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8730 Z= 0.219 Angle : 0.552 18.710 11829 Z= 0.273 Chirality : 0.040 0.137 1331 Planarity : 0.004 0.059 1458 Dihedral : 5.992 83.934 1646 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.12 % Allowed : 19.22 % Favored : 78.66 % 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: 1.04 (0.27), residues: 1024 helix: 2.60 (0.24), residues: 421 sheet: -0.66 (0.33), residues: 221 loop : -0.61 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.017 0.001 TYR N 117 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8543 (mtt) REVERT: R 162 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8204 (p) REVERT: R 270 VAL cc_start: 0.8224 (t) cc_final: 0.7939 (p) REVERT: R 338 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7511 (mtt180) REVERT: A 60 MET cc_start: 0.6340 (ttt) cc_final: 0.6019 (ttt) REVERT: A 146 GLN cc_start: 0.8557 (mm110) cc_final: 0.8349 (mm-40) REVERT: A 170 TYR cc_start: 0.8535 (t80) cc_final: 0.8182 (t80) REVERT: A 202 THR cc_start: 0.8077 (m) cc_final: 0.7783 (p) REVERT: A 225 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7894 (tpp-160) REVERT: A 244 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 20 ASP cc_start: 0.8057 (m-30) cc_final: 0.7690 (m-30) REVERT: B 25 CYS cc_start: 0.8570 (m) cc_final: 0.7919 (p) REVERT: B 153 ASP cc_start: 0.8177 (p0) cc_final: 0.7977 (p0) REVERT: B 160 SER cc_start: 0.8154 (t) cc_final: 0.7940 (p) REVERT: B 197 ARG cc_start: 0.8112 (mmt180) cc_final: 0.7844 (mtt180) REVERT: B 230 ASN cc_start: 0.8404 (m-40) cc_final: 0.7998 (m-40) REVERT: B 239 ASN cc_start: 0.8364 (m-40) cc_final: 0.8069 (m110) REVERT: B 256 ARG cc_start: 0.8575 (mtt90) cc_final: 0.8230 (mtm180) REVERT: N 25 SER cc_start: 0.8262 (t) cc_final: 0.7870 (m) REVERT: N 29 PHE cc_start: 0.8373 (t80) cc_final: 0.8083 (t80) outliers start: 19 outliers final: 12 residues processed: 238 average time/residue: 1.2336 time to fit residues: 311.1498 Evaluate side-chains 240 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 160 GLN A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8730 Z= 0.222 Angle : 0.559 19.590 11829 Z= 0.276 Chirality : 0.040 0.153 1331 Planarity : 0.004 0.058 1458 Dihedral : 5.912 83.159 1646 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.35 % Allowed : 19.66 % Favored : 77.99 % 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: 1.03 (0.27), residues: 1024 helix: 2.69 (0.24), residues: 417 sheet: -0.78 (0.32), residues: 223 loop : -0.64 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.015 0.001 PHE R 51 TYR 0.017 0.001 TYR N 117 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8577 (mtt) REVERT: R 162 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (p) REVERT: R 270 VAL cc_start: 0.8244 (t) cc_final: 0.7949 (p) REVERT: R 333 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 60 MET cc_start: 0.6348 (ttt) cc_final: 0.5975 (ttt) REVERT: A 170 TYR cc_start: 0.8555 (t80) cc_final: 0.8200 (t80) REVERT: A 202 THR cc_start: 0.8075 (m) cc_final: 0.7772 (p) REVERT: A 225 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7891 (tpp-160) REVERT: A 244 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 20 ASP cc_start: 0.8029 (m-30) cc_final: 0.7666 (m-30) REVERT: B 25 CYS cc_start: 0.8573 (m) cc_final: 0.7923 (p) REVERT: B 96 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8651 (mtm-85) REVERT: B 160 SER cc_start: 0.8135 (t) cc_final: 0.7916 (p) REVERT: B 197 ARG cc_start: 0.8132 (mmt180) cc_final: 0.7862 (mtt180) REVERT: B 230 ASN cc_start: 0.8395 (m-40) cc_final: 0.7984 (m-40) REVERT: B 239 ASN cc_start: 0.8363 (m-40) cc_final: 0.8007 (m110) REVERT: B 256 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8364 (mtt90) REVERT: N 25 SER cc_start: 0.8291 (t) cc_final: 0.7890 (m) outliers start: 21 outliers final: 12 residues processed: 234 average time/residue: 1.2731 time to fit residues: 315.4361 Evaluate side-chains 243 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.0070 chunk 85 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8730 Z= 0.177 Angle : 0.540 17.635 11829 Z= 0.268 Chirality : 0.039 0.154 1331 Planarity : 0.004 0.049 1458 Dihedral : 5.790 81.440 1646 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 21.23 % Favored : 77.09 % 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: 1.09 (0.27), residues: 1024 helix: 2.77 (0.24), residues: 417 sheet: -0.75 (0.32), residues: 235 loop : -0.64 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR N 117 ARG 0.007 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: R 162 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8200 (p) REVERT: R 270 VAL cc_start: 0.8212 (t) cc_final: 0.7923 (p) REVERT: A 57 VAL cc_start: 0.8145 (t) cc_final: 0.7903 (m) REVERT: A 60 MET cc_start: 0.6231 (ttt) cc_final: 0.5855 (ttt) REVERT: A 170 TYR cc_start: 0.8541 (t80) cc_final: 0.8204 (t80) REVERT: A 202 THR cc_start: 0.7995 (m) cc_final: 0.7666 (p) REVERT: A 225 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7950 (tpp-160) REVERT: A 244 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8283 (mt-10) REVERT: B 25 CYS cc_start: 0.8565 (m) cc_final: 0.7928 (p) REVERT: B 105 TYR cc_start: 0.8655 (t80) cc_final: 0.8216 (t80) REVERT: B 160 SER cc_start: 0.8127 (t) cc_final: 0.7904 (p) REVERT: B 197 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7865 (mtt180) REVERT: B 230 ASN cc_start: 0.8402 (m-40) cc_final: 0.7986 (m-40) REVERT: B 239 ASN cc_start: 0.8349 (m-40) cc_final: 0.8014 (m110) REVERT: B 256 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8343 (mtt90) REVERT: N 25 SER cc_start: 0.8295 (t) cc_final: 0.7993 (m) REVERT: N 29 PHE cc_start: 0.8330 (t80) cc_final: 0.8006 (t80) outliers start: 15 outliers final: 10 residues processed: 237 average time/residue: 1.2582 time to fit residues: 316.5438 Evaluate side-chains 242 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 80 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123984 restraints weight = 11248.919| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.88 r_work: 0.3399 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8730 Z= 0.290 Angle : 0.599 20.046 11829 Z= 0.292 Chirality : 0.041 0.175 1331 Planarity : 0.004 0.065 1458 Dihedral : 5.921 81.846 1646 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.79 % Allowed : 21.79 % Favored : 76.42 % 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: 0.94 (0.27), residues: 1024 helix: 2.60 (0.24), residues: 417 sheet: -0.86 (0.31), residues: 240 loop : -0.60 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 133 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.002 PHE N 68 TYR 0.018 0.002 TYR N 117 ARG 0.007 0.001 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.28 seconds wall clock time: 83 minutes 45.82 seconds (5025.82 seconds total)