Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 23:25:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2023/7ljc_23390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2023/7ljc_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_23390/04_2023/7ljc_23390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2023/7ljc_23390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2023/7ljc_23390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2023/7ljc_23390.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.12, 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: 3.64 Conformation dependent library (CDL) restraints added in 1.4 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: 0.44 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: 2.38 Time building geometry restraints manager: 3.73 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: 5020 17.55 - 35.09: 114 35.09 - 52.64: 20 52.64 - 70.18: 2 70.18 - 87.73: 2 Dihedral angle restraints: 5158 sinusoidal: 2122 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 5155 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 25.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- 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 : 8.580 87.728 3174 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 % 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 *********************** 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 : 1.042 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 1.0698 time to fit residues: 336.3257 Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1234 time to fit residues: 1.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 91 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: R 41 ASN R 164 HIS R 222 GLN A 19 GLN A 75 GLN A 239 HIS B 62 HIS B 88 ASN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7926 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8730 Z= 0.225 Angle : 0.566 14.679 11829 Z= 0.293 Chirality : 0.041 0.174 1331 Planarity : 0.005 0.048 1458 Dihedral : 5.862 85.997 1278 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1024 helix: 2.31 (0.23), residues: 407 sheet: -0.41 (0.34), residues: 214 loop : -1.34 (0.28), residues: 403 *********************** 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 280 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 264 average time/residue: 1.2312 time to fit residues: 345.4871 Evaluate side-chains 248 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.6900 time to fit residues: 5.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.0030 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8730 Z= 0.207 Angle : 0.545 17.585 11829 Z= 0.279 Chirality : 0.040 0.138 1331 Planarity : 0.004 0.046 1458 Dihedral : 5.493 83.425 1278 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.57 % 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: 0.80 (0.26), residues: 1024 helix: 2.48 (0.24), residues: 418 sheet: -0.39 (0.34), residues: 196 loop : -1.08 (0.28), residues: 410 *********************** 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 261 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 0.879 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 246 average time/residue: 1.1662 time to fit residues: 305.7500 Evaluate side-chains 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 10 average time/residue: 0.6060 time to fit residues: 8.0872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 88 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7955 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8730 Z= 0.180 Angle : 0.522 18.072 11829 Z= 0.262 Chirality : 0.039 0.130 1331 Planarity : 0.004 0.047 1458 Dihedral : 5.308 81.996 1278 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.12 % 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 (0.26), residues: 1024 helix: 2.65 (0.25), residues: 419 sheet: -0.42 (0.33), residues: 196 loop : -0.81 (0.30), residues: 409 *********************** 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 256 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 247 average time/residue: 1.1913 time to fit residues: 312.8772 Evaluate side-chains 242 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.3294 time to fit residues: 3.7787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 17 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 8730 Z= 0.317 Angle : 0.577 18.143 11829 Z= 0.288 Chirality : 0.041 0.138 1331 Planarity : 0.004 0.064 1458 Dihedral : 5.596 84.005 1278 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.68 % 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: 0.96 (0.26), residues: 1024 helix: 2.41 (0.24), residues: 418 sheet: -0.47 (0.33), residues: 216 loop : -0.63 (0.32), residues: 390 *********************** 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 273 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 249 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 257 average time/residue: 1.1874 time to fit residues: 324.6309 Evaluate side-chains 251 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 7 average time/residue: 0.2684 time to fit residues: 3.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 88 ASN ** B 259 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3703 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= 0.218 Angle : 0.553 19.220 11829 Z= 0.272 Chirality : 0.040 0.132 1331 Planarity : 0.004 0.060 1458 Dihedral : 5.409 82.108 1278 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.23 % 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: 0.99 (0.26), residues: 1024 helix: 2.51 (0.24), residues: 418 sheet: -0.60 (0.33), residues: 214 loop : -0.63 (0.31), residues: 392 *********************** 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 252 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 241 average time/residue: 1.2422 time to fit residues: 318.5616 Evaluate side-chains 230 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.1560 time to fit residues: 2.2426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 8730 Z= 0.291 Angle : 0.573 19.666 11829 Z= 0.282 Chirality : 0.041 0.140 1331 Planarity : 0.004 0.063 1458 Dihedral : 5.470 82.580 1278 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.68 % 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: 0.95 (0.26), residues: 1024 helix: 2.42 (0.24), residues: 417 sheet: -0.59 (0.33), residues: 222 loop : -0.59 (0.32), residues: 385 *********************** 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 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 0.882 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 240 average time/residue: 1.2948 time to fit residues: 330.7049 Evaluate side-chains 238 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.3666 time to fit residues: 3.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 8730 Z= 0.229 Angle : 0.559 19.165 11829 Z= 0.276 Chirality : 0.040 0.133 1331 Planarity : 0.004 0.058 1458 Dihedral : 5.343 80.688 1278 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1024 helix: 2.50 (0.24), residues: 419 sheet: -0.61 (0.33), residues: 222 loop : -0.55 (0.32), residues: 383 *********************** 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 246 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 0.934 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 240 average time/residue: 1.2851 time to fit residues: 327.5777 Evaluate side-chains 239 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.9241 time to fit residues: 4.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 259 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 8730 Z= 0.282 Angle : 0.595 19.606 11829 Z= 0.291 Chirality : 0.041 0.152 1331 Planarity : 0.004 0.061 1458 Dihedral : 5.422 80.683 1278 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.23 % 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: 0.95 (0.27), residues: 1024 helix: 2.50 (0.24), residues: 413 sheet: -0.74 (0.33), residues: 222 loop : -0.53 (0.32), residues: 389 *********************** 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 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 0.978 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 240 average time/residue: 1.2279 time to fit residues: 313.1891 Evaluate side-chains 247 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.6228 time to fit residues: 4.8489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 8730 Z= 0.207 Angle : 0.587 19.195 11829 Z= 0.287 Chirality : 0.040 0.147 1331 Planarity : 0.004 0.052 1458 Dihedral : 5.280 78.158 1278 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.45 % 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: 0.93 (0.27), residues: 1024 helix: 2.50 (0.24), residues: 417 sheet: -0.82 (0.32), residues: 231 loop : -0.53 (0.33), residues: 376 ********************** 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 227 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 1.041 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 223 average time/residue: 1.3247 time to fit residues: 312.5845 Evaluate side-chains 222 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 211 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.8393 time to fit residues: 4.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.0040 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 70 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127401 restraints weight = 11343.644| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.93 r_work: 0.3483 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8730 Z= 0.172 Angle : 0.571 18.187 11829 Z= 0.281 Chirality : 0.039 0.157 1331 Planarity : 0.004 0.044 1458 Dihedral : 5.136 75.778 1278 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.90 % 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: 0.95 (0.27), residues: 1024 helix: 2.54 (0.24), residues: 417 sheet: -0.89 (0.31), residues: 239 loop : -0.49 (0.34), residues: 368 =============================================================================== Job complete usr+sys time: 4778.18 seconds wall clock time: 84 minutes 52.59 seconds (5092.59 seconds total)