Starting phenix.real_space_refine on Wed Sep 25 03:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/09_2024/6uva_20906.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6095 2.51 5 N 1657 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9561 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 4, 'TRANS': 38} Chain: "R" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2819 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 4 Time building chain proxies: 5.80, per 1000 atoms: 0.61 Number of scatterers: 9561 At special positions: 0 Unit cell: (115.37, 97.11, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1737 8.00 N 1657 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 15 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 40.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.803A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.637A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.746A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.788A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.509A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.714A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.188A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.632A pdb=" N TRP E 56 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.531A pdb=" N GLY E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 142 Proline residue: E 126 - end of helix removed outlier: 3.951A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.551A pdb=" N CYS R 127 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 167 removed outlier: 3.707A pdb=" N LYS R 134 " --> pdb=" O ASN R 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 204 through 208 removed outlier: 4.205A pdb=" N THR R 207 " --> pdb=" O LEU R 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN R 208 " --> pdb=" O VAL R 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 204 through 208' Processing helix chain 'R' and resid 210 through 242 Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 277 Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.670A pdb=" N TRP R 283 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 321 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 350 Processing helix chain 'R' and resid 363 through 385 removed outlier: 5.205A pdb=" N GLY R 377 " --> pdb=" O MET R 373 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU R 378 " --> pdb=" O HIS R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.970A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.528A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.501A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.202A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.775A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.634A 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: 6.523A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.527A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.672A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 84 through 87 456 hydrogen bonds defined for protein. 1293 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: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3099 1.34 - 1.46: 2237 1.46 - 1.58: 4344 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 9780 Sorted by residual: bond pdb=" C ASP P 40 " pdb=" N PRO P 41 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.30e-01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.45e-01 bond pdb=" CA GLU E 74 " pdb=" C GLU E 74 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.28e-02 6.10e+03 6.82e-01 bond pdb=" C VAL E 124 " pdb=" N ILE E 125 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.13e-02 7.83e+03 6.31e-01 bond pdb=" CA VAL E 51 " pdb=" CB VAL E 51 " ideal model delta sigma weight residual 1.538 1.546 -0.008 1.10e-02 8.26e+03 5.83e-01 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 13037 1.66 - 3.32: 181 3.32 - 4.98: 33 4.98 - 6.64: 9 6.64 - 8.31: 2 Bond angle restraints: 13262 Sorted by residual: angle pdb=" CA TYR R 367 " pdb=" CB TYR R 367 " pdb=" CG TYR R 367 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" N VAL R 205 " pdb=" CA VAL R 205 " pdb=" C VAL R 205 " ideal model delta sigma weight residual 112.29 109.46 2.83 9.40e-01 1.13e+00 9.08e+00 angle pdb=" C THR E 73 " pdb=" N GLU E 74 " pdb=" CA GLU E 74 " ideal model delta sigma weight residual 122.37 118.02 4.35 1.54e+00 4.22e-01 7.97e+00 angle pdb=" C PHE R 166 " pdb=" N LYS R 167 " pdb=" CA LYS R 167 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.81e+00 angle pdb=" CA LEU R 395 " pdb=" CB LEU R 395 " pdb=" CG LEU R 395 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.63e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4970 17.98 - 35.96: 561 35.96 - 53.94: 193 53.94 - 71.92: 49 71.92 - 89.89: 15 Dihedral angle restraints: 5788 sinusoidal: 2300 harmonic: 3488 Sorted by residual: dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -167.11 81.11 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 142.59 -49.59 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 74 " pdb=" CB CYS R 74 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 915 0.030 - 0.060: 377 0.060 - 0.091: 109 0.091 - 0.121: 68 0.121 - 0.151: 6 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA LYS E 42 " pdb=" N LYS E 42 " pdb=" C LYS E 42 " pdb=" CB LYS E 42 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE R 352 " pdb=" N ILE R 352 " pdb=" C ILE R 352 " pdb=" CB ILE R 352 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE E 123 " pdb=" N ILE E 123 " pdb=" C ILE E 123 " pdb=" CB ILE E 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1472 not shown) Planarity restraints: 1684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 367 " 0.016 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR R 367 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 367 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 114 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO E 115 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO E 114 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.017 5.00e-02 4.00e+02 ... (remaining 1681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9414 3.28 - 3.82: 16408 3.82 - 4.36: 19653 4.36 - 4.90: 32748 Nonbonded interactions: 79110 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O TRP R 72 " pdb=" OH TYR R 91 " model vdw 2.296 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.318 3.040 nonbonded pdb=" O HIS R 370 " pdb=" ND1 HIS R 374 " model vdw 2.321 3.120 ... (remaining 79105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 1.190 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9780 Z= 0.140 Angle : 0.547 8.305 13262 Z= 0.313 Chirality : 0.040 0.151 1475 Planarity : 0.003 0.033 1684 Dihedral : 18.040 89.894 3503 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.36 % Allowed : 26.30 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.22), residues: 1169 helix: -0.89 (0.22), residues: 434 sheet: -1.42 (0.30), residues: 225 loop : -2.05 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS R 374 PHE 0.011 0.001 PHE R 308 TYR 0.030 0.001 TYR R 367 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.064 Fit side-chains REVERT: A 17 LYS cc_start: 0.5897 (pmtt) cc_final: 0.5426 (mmtm) REVERT: B 96 ARG cc_start: 0.6594 (mtm180) cc_final: 0.6373 (mtm110) REVERT: B 134 ARG cc_start: 0.6435 (ptp-110) cc_final: 0.6043 (ppt170) REVERT: E 142 LYS cc_start: 0.5737 (mtmp) cc_final: 0.5497 (mtmt) REVERT: R 42 MET cc_start: 0.3583 (mtm) cc_final: 0.3213 (ttm) REVERT: R 339 LEU cc_start: 0.7314 (mp) cc_final: 0.7093 (mm) outliers start: 35 outliers final: 9 residues processed: 164 average time/residue: 1.4577 time to fit residues: 253.4135 Evaluate side-chains 115 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0370 chunk 68 optimal weight: 0.0170 chunk 106 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 88 ASN B 259 GLN E 86 ASN E 110 HIS ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9780 Z= 0.153 Angle : 0.546 7.820 13262 Z= 0.289 Chirality : 0.042 0.152 1475 Planarity : 0.004 0.036 1684 Dihedral : 5.265 49.506 1312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.93 % Allowed : 25.24 % Favored : 70.83 % 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: -1.13 (0.24), residues: 1169 helix: 0.31 (0.24), residues: 441 sheet: -0.88 (0.31), residues: 232 loop : -1.60 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 56 HIS 0.005 0.001 HIS R 374 PHE 0.015 0.001 PHE E 100 TYR 0.009 0.001 TYR R 227 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.138 Fit side-chains REVERT: A 31 GLN cc_start: 0.6923 (tp-100) cc_final: 0.6719 (tp40) REVERT: A 216 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.5999 (mppt) REVERT: B 44 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6419 (mt0) REVERT: B 96 ARG cc_start: 0.6701 (mtm180) cc_final: 0.6456 (mtm110) REVERT: B 134 ARG cc_start: 0.6535 (ptp-110) cc_final: 0.6009 (ppt170) REVERT: N 67 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6303 (ttp80) REVERT: N 85 SER cc_start: 0.6528 (m) cc_final: 0.6092 (m) REVERT: P 18 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: R 42 MET cc_start: 0.3663 (mtm) cc_final: 0.3312 (ttm) REVERT: R 53 MET cc_start: 0.2903 (ptm) cc_final: 0.2208 (ptm) outliers start: 41 outliers final: 9 residues processed: 148 average time/residue: 1.3879 time to fit residues: 218.4607 Evaluate side-chains 120 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 357 HIS B 259 GLN B 266 HIS N 35 ASN N 82 GLN E 71 ASN E 86 ASN E 97 HIS ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9780 Z= 0.171 Angle : 0.559 6.887 13262 Z= 0.296 Chirality : 0.043 0.144 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.651 27.441 1299 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.09 % Allowed : 24.57 % Favored : 70.35 % 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: -0.47 (0.24), residues: 1169 helix: 0.91 (0.25), residues: 443 sheet: -0.49 (0.31), residues: 241 loop : -1.34 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 84 HIS 0.010 0.001 HIS E 97 PHE 0.012 0.001 PHE E 100 TYR 0.010 0.001 TYR R 227 ARG 0.005 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 117 time to evaluate : 1.091 Fit side-chains REVERT: A 216 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6030 (mppt) REVERT: A 278 ASN cc_start: 0.8146 (m-40) cc_final: 0.7896 (m110) REVERT: B 59 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 134 ARG cc_start: 0.6565 (ptp-110) cc_final: 0.5969 (ppt170) REVERT: B 146 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7939 (mm) REVERT: B 219 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7262 (mtt180) REVERT: B 266 HIS cc_start: 0.7063 (t-90) cc_final: 0.6845 (t70) REVERT: E 75 MET cc_start: 0.2266 (OUTLIER) cc_final: 0.1788 (mpm) REVERT: E 97 HIS cc_start: 0.2654 (OUTLIER) cc_final: 0.2437 (t-170) REVERT: E 118 VAL cc_start: 0.5630 (t) cc_final: 0.5289 (t) REVERT: R 42 MET cc_start: 0.3670 (mtm) cc_final: 0.3394 (ttm) REVERT: R 53 MET cc_start: 0.2879 (ptm) cc_final: 0.2285 (ptm) REVERT: R 287 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6617 (t0) outliers start: 53 outliers final: 15 residues processed: 159 average time/residue: 1.3037 time to fit residues: 221.0760 Evaluate side-chains 133 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 267 GLN A 357 HIS B 32 GLN B 155 ASN B 176 GLN N 35 ASN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9780 Z= 0.153 Angle : 0.534 6.768 13262 Z= 0.283 Chirality : 0.042 0.142 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.578 25.993 1299 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.61 % Allowed : 25.05 % Favored : 70.35 % 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: -0.17 (0.25), residues: 1169 helix: 1.16 (0.25), residues: 443 sheet: -0.19 (0.33), residues: 236 loop : -1.24 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 139 HIS 0.005 0.001 HIS R 374 PHE 0.012 0.001 PHE R 262 TYR 0.019 0.001 TYR N 60 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.108 Fit side-chains REVERT: B 59 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: B 134 ARG cc_start: 0.6427 (ptp-110) cc_final: 0.5860 (ppt170) REVERT: B 146 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 266 HIS cc_start: 0.7178 (t-90) cc_final: 0.6878 (t70) REVERT: E 75 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1654 (mpm) REVERT: E 118 VAL cc_start: 0.5652 (OUTLIER) cc_final: 0.5300 (t) REVERT: E 140 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.4188 (mmm160) REVERT: R 42 MET cc_start: 0.3684 (mtm) cc_final: 0.3382 (ttm) REVERT: R 53 MET cc_start: 0.2982 (ptm) cc_final: 0.2368 (ptm) REVERT: R 136 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5213 (mtmm) REVERT: R 287 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6647 (t0) REVERT: R 339 LEU cc_start: 0.7310 (mp) cc_final: 0.7075 (mm) outliers start: 48 outliers final: 20 residues processed: 151 average time/residue: 1.3027 time to fit residues: 209.8983 Evaluate side-chains 136 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS A 387 HIS B 176 GLN B 220 GLN B 340 ASN G 59 ASN E 86 ASN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN R 187 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9780 Z= 0.301 Angle : 0.685 7.712 13262 Z= 0.369 Chirality : 0.048 0.231 1475 Planarity : 0.005 0.045 1684 Dihedral : 5.454 30.317 1299 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.47 % Allowed : 24.47 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.39 (0.24), residues: 1169 helix: 0.83 (0.24), residues: 446 sheet: -0.43 (0.31), residues: 249 loop : -1.14 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 139 HIS 0.006 0.002 HIS B 54 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.002 TYR A 391 ARG 0.008 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 105 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6323 (mt-10) cc_final: 0.6058 (mt-10) REVERT: A 216 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5822 (mmtm) REVERT: A 317 ARG cc_start: 0.5093 (mmt-90) cc_final: 0.4506 (tpp80) REVERT: B 46 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.7008 (mtt-85) REVERT: B 59 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 266 HIS cc_start: 0.7262 (t-90) cc_final: 0.6922 (t70) REVERT: N 123 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7631 (tp-100) REVERT: E 75 MET cc_start: 0.2368 (OUTLIER) cc_final: 0.1667 (mpm) REVERT: E 140 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.5399 (mmm160) REVERT: P 18 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7384 (tp40) REVERT: R 42 MET cc_start: 0.3754 (mtm) cc_final: 0.3438 (ttm) REVERT: R 287 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6676 (t0) REVERT: R 333 LYS cc_start: 0.5407 (mttp) cc_final: 0.4983 (mmtt) REVERT: R 339 LEU cc_start: 0.7442 (mp) cc_final: 0.7203 (mm) outliers start: 57 outliers final: 24 residues processed: 146 average time/residue: 1.4110 time to fit residues: 221.1612 Evaluate side-chains 130 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.167 Angle : 0.563 6.658 13262 Z= 0.298 Chirality : 0.043 0.148 1475 Planarity : 0.004 0.041 1684 Dihedral : 4.979 31.364 1299 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.22 % Allowed : 25.62 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.05 (0.25), residues: 1169 helix: 1.26 (0.25), residues: 439 sheet: -0.35 (0.32), residues: 244 loop : -1.03 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 139 HIS 0.010 0.001 HIS E 97 PHE 0.013 0.001 PHE B 199 TYR 0.022 0.001 TYR N 60 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 1.092 Fit side-chains REVERT: A 209 GLU cc_start: 0.6192 (mt-10) cc_final: 0.5900 (mt-10) REVERT: A 216 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5952 (mmtm) REVERT: B 59 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: B 146 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 266 HIS cc_start: 0.7240 (t-90) cc_final: 0.6951 (t70) REVERT: E 62 PHE cc_start: 0.2055 (OUTLIER) cc_final: 0.1492 (p90) REVERT: E 75 MET cc_start: 0.2414 (OUTLIER) cc_final: 0.1256 (tmm) REVERT: E 140 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.4120 (mmm160) REVERT: R 287 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6682 (t0) REVERT: R 333 LYS cc_start: 0.5254 (mttp) cc_final: 0.4886 (mmpt) REVERT: R 339 LEU cc_start: 0.7369 (mp) cc_final: 0.7133 (mm) REVERT: R 390 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5999 (mt-10) outliers start: 44 outliers final: 17 residues processed: 140 average time/residue: 1.3389 time to fit residues: 199.8975 Evaluate side-chains 124 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN B 259 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9780 Z= 0.208 Angle : 0.596 7.238 13262 Z= 0.318 Chirality : 0.044 0.149 1475 Planarity : 0.004 0.044 1684 Dihedral : 5.083 31.332 1298 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.03 % Allowed : 26.39 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.05 (0.25), residues: 1169 helix: 1.18 (0.25), residues: 446 sheet: -0.29 (0.32), residues: 243 loop : -0.99 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 139 HIS 0.008 0.001 HIS E 97 PHE 0.013 0.002 PHE B 199 TYR 0.020 0.001 TYR N 60 ARG 0.005 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 1.102 Fit side-chains REVERT: A 216 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5902 (mmtm) REVERT: B 46 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6984 (mmt-90) REVERT: B 59 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: B 146 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7981 (mm) REVERT: B 266 HIS cc_start: 0.7224 (t-90) cc_final: 0.6978 (t70) REVERT: N 67 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6330 (ttp80) REVERT: E 62 PHE cc_start: 0.2143 (OUTLIER) cc_final: 0.1588 (p90) REVERT: E 75 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.1378 (tmm) REVERT: E 140 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.4199 (mmm160) REVERT: P 18 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: R 287 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6647 (t0) REVERT: R 333 LYS cc_start: 0.5320 (mttp) cc_final: 0.4921 (mmpt) REVERT: R 369 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5365 (mmt) REVERT: R 390 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.6008 (mt-10) outliers start: 42 outliers final: 21 residues processed: 129 average time/residue: 1.3768 time to fit residues: 189.2617 Evaluate side-chains 129 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9780 Z= 0.328 Angle : 0.714 9.508 13262 Z= 0.383 Chirality : 0.049 0.202 1475 Planarity : 0.005 0.045 1684 Dihedral : 5.662 32.452 1298 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.74 % Allowed : 26.10 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.28 (0.24), residues: 1169 helix: 0.97 (0.24), residues: 434 sheet: -0.32 (0.33), residues: 235 loop : -1.10 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 139 HIS 0.007 0.002 HIS R 374 PHE 0.015 0.002 PHE B 199 TYR 0.022 0.002 TYR N 60 ARG 0.008 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5839 (mmtm) REVERT: B 59 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: B 146 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8058 (mm) REVERT: N 67 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6426 (ttp80) REVERT: E 75 MET cc_start: 0.2495 (OUTLIER) cc_final: 0.1681 (mpm) REVERT: P 18 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: R 287 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6622 (t0) REVERT: R 333 LYS cc_start: 0.5495 (mttp) cc_final: 0.5015 (mmtt) REVERT: R 369 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5305 (mmt) REVERT: R 375 PHE cc_start: 0.7078 (m-10) cc_final: 0.6697 (m-80) REVERT: R 390 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5999 (mt-10) outliers start: 39 outliers final: 24 residues processed: 131 average time/residue: 1.4150 time to fit residues: 197.4422 Evaluate side-chains 128 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.0040 chunk 104 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 266 HIS E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9780 Z= 0.184 Angle : 0.589 7.398 13262 Z= 0.313 Chirality : 0.043 0.147 1475 Planarity : 0.004 0.044 1684 Dihedral : 5.177 31.355 1298 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.74 % Allowed : 26.49 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.05 (0.25), residues: 1169 helix: 1.28 (0.25), residues: 434 sheet: -0.29 (0.32), residues: 236 loop : -1.05 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 139 HIS 0.008 0.001 HIS E 97 PHE 0.013 0.002 PHE R 262 TYR 0.027 0.001 TYR N 60 ARG 0.005 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 96 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5891 (mmtm) REVERT: B 59 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: B 146 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7964 (mm) REVERT: B 266 HIS cc_start: 0.7226 (t-90) cc_final: 0.6879 (t70) REVERT: N 67 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6454 (ttp80) REVERT: E 140 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4144 (mmm160) REVERT: P 18 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: R 287 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6615 (t0) REVERT: R 333 LYS cc_start: 0.5315 (mttp) cc_final: 0.4885 (mmpt) REVERT: R 369 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5349 (mmt) REVERT: R 390 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.6029 (mt-10) outliers start: 39 outliers final: 21 residues processed: 128 average time/residue: 1.4249 time to fit residues: 193.5358 Evaluate side-chains 125 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.0980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.175 Angle : 0.582 7.012 13262 Z= 0.308 Chirality : 0.043 0.146 1475 Planarity : 0.004 0.045 1684 Dihedral : 5.007 30.183 1298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.07 % Allowed : 27.26 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.00 (0.25), residues: 1169 helix: 1.28 (0.25), residues: 440 sheet: -0.29 (0.32), residues: 241 loop : -0.99 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 139 HIS 0.008 0.001 HIS E 97 PHE 0.013 0.001 PHE R 262 TYR 0.027 0.001 TYR N 60 ARG 0.006 0.000 ARG E 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5990 (mt-10) REVERT: A 216 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6021 (mmtm) REVERT: B 59 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 146 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 266 HIS cc_start: 0.7311 (t-90) cc_final: 0.7047 (t70) REVERT: N 67 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6397 (ttp80) REVERT: E 62 PHE cc_start: 0.2268 (OUTLIER) cc_final: 0.1612 (p90) REVERT: E 75 MET cc_start: 0.2829 (mmp) cc_final: 0.2023 (tmm) REVERT: E 140 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.4120 (mmm160) REVERT: R 287 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6658 (t0) REVERT: R 333 LYS cc_start: 0.5354 (mttp) cc_final: 0.4954 (mmpt) REVERT: R 339 LEU cc_start: 0.7394 (mp) cc_final: 0.7123 (mm) REVERT: R 369 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5378 (mmt) REVERT: R 390 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6032 (mt-10) outliers start: 32 outliers final: 18 residues processed: 126 average time/residue: 1.4702 time to fit residues: 196.5740 Evaluate side-chains 124 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.214955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169446 restraints weight = 9625.471| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.41 r_work: 0.3737 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9780 Z= 0.192 Angle : 0.598 7.092 13262 Z= 0.316 Chirality : 0.044 0.152 1475 Planarity : 0.004 0.045 1684 Dihedral : 5.080 29.940 1298 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.26 % Allowed : 27.06 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1169 helix: 1.30 (0.25), residues: 439 sheet: -0.28 (0.32), residues: 241 loop : -0.98 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 139 HIS 0.008 0.001 HIS E 97 PHE 0.012 0.002 PHE B 199 TYR 0.025 0.001 TYR N 60 ARG 0.006 0.000 ARG E 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4194.87 seconds wall clock time: 76 minutes 56.53 seconds (4616.53 seconds total)