Starting phenix.real_space_refine on Fri Dec 8 14:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/12_2023/7ljc_23390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/12_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_23390/12_2023/7ljc_23390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/12_2023/7ljc_23390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/12_2023/7ljc_23390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/12_2023/7ljc_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.25, per 1000 atoms: 0.61 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: 3.40 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: 0.88 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: 2.37 Time building geometry restraints manager: 3.66 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: 0.370 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: 1.750 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.440 Find NCS groups from input model: 0.240 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- 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 : 0.870 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 1.0563 time to fit residues: 332.4030 Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1220 time to fit residues: 1.4080 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.2330 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= 0.229 Angle : 0.568 14.651 11829 Z= 0.294 Chirality : 0.041 0.177 1331 Planarity : 0.005 0.049 1458 Dihedral : 7.555 87.102 1645 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 12.85 % Favored : 84.13 % 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: 0.45 (0.25), residues: 1024 helix: 2.24 (0.23), residues: 407 sheet: -0.42 (0.34), residues: 214 loop : -1.35 (0.28), residues: 403 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 0.021 0.002 PHE B 199 TYR 0.014 0.002 TYR B 124 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 284 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 257 time to evaluate : 1.034 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 267 average time/residue: 1.1624 time to fit residues: 330.5303 Evaluate side-chains 246 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 234 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 6 average time/residue: 0.6939 time to fit residues: 5.8589 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN 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: 0.7932 moved from start: 0.2819 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= 0.186 Angle : 0.544 17.818 11829 Z= 0.277 Chirality : 0.040 0.138 1331 Planarity : 0.005 0.120 1458 Dihedral : 7.032 85.104 1645 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.79 % Allowed : 14.75 % Favored : 82.46 % 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: 0.87 (0.26), residues: 1024 helix: 2.59 (0.24), residues: 412 sheet: -0.29 (0.34), residues: 204 loop : -1.10 (0.28), residues: 408 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 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR A 163 ARG 0.009 0.001 ARG A 241 *********************** 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 263 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 246 average time/residue: 1.1163 time to fit residues: 293.2635 Evaluate side-chains 250 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 235 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 8 average time/residue: 0.6100 time to fit residues: 6.7370 ------------------------------------------------------------------------------- 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: 0.0870 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 130 ASN A 236 GLN B 17 GLN B 239 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3255 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= 0.209 Angle : 0.532 18.242 11829 Z= 0.269 Chirality : 0.040 0.129 1331 Planarity : 0.004 0.061 1458 Dihedral : 6.471 84.563 1645 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.23 % Allowed : 16.98 % Favored : 80.78 % 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: 2.55 (0.25), residues: 418 sheet: -0.41 (0.33), residues: 196 loop : -0.83 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 133 HIS 0.006 0.001 HIS A 82 PHE 0.016 0.001 PHE B 199 TYR 0.016 0.002 TYR N 117 ARG 0.009 0.001 ARG B 96 *********************** 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 263 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 252 average time/residue: 1.2106 time to fit residues: 324.5999 Evaluate side-chains 252 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 6 average time/residue: 0.4837 time to fit residues: 4.6637 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 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 ** 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: 0.7988 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8730 Z= 0.236 Angle : 0.539 16.969 11829 Z= 0.272 Chirality : 0.040 0.134 1331 Planarity : 0.004 0.058 1458 Dihedral : 6.227 84.395 1645 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 17.09 % Favored : 80.00 % 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: 2.52 (0.25), residues: 418 sheet: -0.36 (0.34), residues: 208 loop : -0.66 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.006 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.017 0.002 TYR N 117 ARG 0.008 0.001 ARG B 96 *********************** 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 258 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 243 average time/residue: 1.2250 time to fit residues: 316.1645 Evaluate side-chains 237 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 9 average time/residue: 0.3503 time to fit residues: 4.9964 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3666 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= 0.178 Angle : 0.531 19.819 11829 Z= 0.262 Chirality : 0.039 0.131 1331 Planarity : 0.004 0.046 1458 Dihedral : 5.996 82.675 1645 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.91 % Allowed : 18.66 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1024 helix: 2.61 (0.25), residues: 419 sheet: -0.51 (0.32), residues: 226 loop : -0.58 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR N 117 ARG 0.008 0.000 ARG B 96 *********************** 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: 26 poor density : 229 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 238 average time/residue: 1.2206 time to fit residues: 309.0610 Evaluate side-chains 229 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 9 average time/residue: 0.4554 time to fit residues: 6.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 0.8010 moved from start: 0.3839 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= 0.294 Angle : 0.577 19.705 11829 Z= 0.286 Chirality : 0.041 0.141 1331 Planarity : 0.004 0.062 1458 Dihedral : 6.038 83.959 1645 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 20.11 % Favored : 77.77 % 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 (0.27), residues: 1024 helix: 2.45 (0.25), residues: 419 sheet: -0.54 (0.33), residues: 227 loop : -0.59 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 133 HIS 0.006 0.001 HIS A 209 PHE 0.013 0.002 PHE R 288 TYR 0.018 0.002 TYR B 105 ARG 0.007 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 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 239 average time/residue: 1.2378 time to fit residues: 314.5369 Evaluate side-chains 231 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.2537 time to fit residues: 6.6442 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8730 Z= 0.241 Angle : 0.575 19.724 11829 Z= 0.284 Chirality : 0.040 0.144 1331 Planarity : 0.004 0.058 1458 Dihedral : 5.938 83.125 1645 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.90 % Allowed : 21.01 % 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: 0.98 (0.27), residues: 1024 helix: 2.55 (0.24), residues: 413 sheet: -0.67 (0.32), residues: 229 loop : -0.59 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.005 0.001 HIS A 209 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.002 TYR B 105 ARG 0.006 0.000 ARG B 96 *********************** 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 234 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 226 average time/residue: 1.3055 time to fit residues: 312.9295 Evaluate side-chains 224 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.4085 time to fit residues: 2.7701 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 17 GLN B 75 GLN B 88 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8730 Z= 0.279 Angle : 0.596 19.517 11829 Z= 0.296 Chirality : 0.041 0.154 1331 Planarity : 0.004 0.060 1458 Dihedral : 5.939 83.367 1645 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.01 % Allowed : 21.56 % 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: 0.86 (0.27), residues: 1024 helix: 2.42 (0.24), residues: 413 sheet: -0.78 (0.32), residues: 232 loop : -0.57 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.006 0.001 HIS A 209 PHE 0.014 0.002 PHE R 288 TYR 0.018 0.002 TYR N 117 ARG 0.007 0.001 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 250 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 239 average time/residue: 1.2779 time to fit residues: 325.2134 Evaluate side-chains 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.4727 time to fit residues: 4.4655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 17 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 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: 0.7978 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8730 Z= 0.189 Angle : 0.571 18.722 11829 Z= 0.284 Chirality : 0.040 0.138 1331 Planarity : 0.004 0.050 1458 Dihedral : 5.771 81.026 1645 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.56 % Allowed : 22.57 % Favored : 75.87 % 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: 2.52 (0.24), residues: 415 sheet: -0.78 (0.32), residues: 231 loop : -0.54 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 133 HIS 0.004 0.001 HIS A 82 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.002 TYR N 117 ARG 0.008 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 224 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 1.4074 time to fit residues: 322.5993 Evaluate side-chains 226 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.3178 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124293 restraints weight = 11305.586| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.88 r_work: 0.3449 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8730 Z= 0.258 Angle : 0.596 18.739 11829 Z= 0.296 Chirality : 0.041 0.163 1331 Planarity : 0.004 0.056 1458 Dihedral : 5.856 81.255 1645 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.45 % Allowed : 23.13 % Favored : 75.42 % 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: 0.91 (0.27), residues: 1024 helix: 2.47 (0.24), residues: 415 sheet: -0.81 (0.32), residues: 227 loop : -0.55 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 133 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.002 PHE N 68 TYR 0.018 0.002 TYR N 117 ARG 0.008 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.97 seconds wall clock time: 86 minutes 15.51 seconds (5175.51 seconds total)