Starting phenix.real_space_refine on Wed Feb 14 00:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f53_31456/02_2024/7f53_31456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f53_31456/02_2024/7f53_31456.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/7f53_31456/02_2024/7f53_31456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f53_31456/02_2024/7f53_31456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f53_31456/02_2024/7f53_31456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f53_31456/02_2024/7f53_31456.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= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 63 5.16 5 C 5165 2.51 5 N 1407 2.21 5 O 1517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R GLU 315": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8153 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "L" Number of atoms: 133 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 13, 114 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Conformer: "C" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain breaks: 1 bond proxies already assigned to first conformer: 98 Conformer: "B" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain breaks: 1 bond proxies already assigned to first conformer: 98 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU L 5 " occ=0.45 ... (16 atoms not shown) pdb=" OE2CGLU L 5 " occ=0.55 residue: pdb=" N AHIS L 6 " occ=0.20 ... (18 atoms not shown) pdb=" NE2BHIS L 6 " occ=0.80 Time building chain proxies: 5.13, per 1000 atoms: 0.63 Number of scatterers: 8153 At special positions: 0 Unit cell: (86.19, 95.316, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 63 16.00 O 1517 8.00 N 1407 7.00 C 5165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.04 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " 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: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.593A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.997A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.727A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.459A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.921A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.526A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 72 removed outlier: 3.809A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 Processing helix chain 'R' and resid 117 through 153 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 192 through 228 removed outlier: 3.749A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.802A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.603A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.772A pdb=" N ILE R 289 " --> pdb=" O ASN R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 301 No H-bonds generated for 'chain 'R' and resid 299 through 301' Processing helix chain 'R' and resid 302 through 305 removed outlier: 3.565A pdb=" N ARG R 305 " --> pdb=" O TYR R 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 302 through 305' Processing helix chain 'R' and resid 306 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.332A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.804A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.600A 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 63 removed outlier: 3.582A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.511A 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: 4.155A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.565A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.803A 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: 3.668A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.147A 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: 6.680A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.635A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.687A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1281 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: 2.67 Time building geometry restraints manager: 3.44 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: 2141 1.33 - 1.45: 1814 1.45 - 1.58: 4261 1.58 - 1.70: 0 1.70 - 1.83: 89 Bond restraints: 8305 Sorted by residual: bond pdb=" C VAL A 287 " pdb=" O VAL A 287 " ideal model delta sigma weight residual 1.238 1.207 0.031 1.10e-02 8.26e+03 7.79e+00 bond pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.30e+00 bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.07e-02 8.73e+03 3.72e+00 bond pdb=" CG LEU B 318 " pdb=" CD2 LEU B 318 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CA ASN R 72 " pdb=" C ASN R 72 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.26e-02 6.30e+03 2.82e+00 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.35: 118 105.35 - 112.55: 4286 112.55 - 119.75: 2839 119.75 - 126.96: 3901 126.96 - 134.16: 96 Bond angle restraints: 11240 Sorted by residual: angle pdb=" N ASN R 72 " pdb=" CA ASN R 72 " pdb=" C ASN R 72 " ideal model delta sigma weight residual 108.67 115.27 -6.60 1.55e+00 4.16e-01 1.81e+01 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" C VAL A 287 " ideal model delta sigma weight residual 107.75 113.84 -6.09 1.46e+00 4.69e-01 1.74e+01 angle pdb=" N ASN R 294 " pdb=" CA ASN R 294 " pdb=" C ASN R 294 " ideal model delta sigma weight residual 111.36 106.92 4.44 1.09e+00 8.42e-01 1.66e+01 angle pdb=" N TYR R 157 " pdb=" CA TYR R 157 " pdb=" C TYR R 157 " ideal model delta sigma weight residual 110.80 119.22 -8.42 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N ALA B 326 " pdb=" CA ALA B 326 " pdb=" C ALA B 326 " ideal model delta sigma weight residual 109.07 114.60 -5.53 1.52e+00 4.33e-01 1.32e+01 ... (remaining 11235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.94: 4840 27.94 - 55.89: 112 55.89 - 83.83: 14 83.83 - 111.78: 2 111.78 - 139.72: 1 Dihedral angle restraints: 4969 sinusoidal: 1954 harmonic: 3015 Sorted by residual: dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -42.91 -43.09 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CGLU L 5 " pdb=" CG CGLU L 5 " pdb=" CD CGLU L 5 " pdb=" OE1CGLU L 5 " ideal model delta sinusoidal sigma weight residual 0.00 139.72 -139.72 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA TRP R 258 " pdb=" C TRP R 258 " pdb=" N ALA R 259 " pdb=" CA ALA R 259 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 906 0.057 - 0.115: 310 0.115 - 0.172: 57 0.172 - 0.229: 4 0.229 - 0.287: 5 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA TYR R 157 " pdb=" N TYR R 157 " pdb=" C TYR R 157 " pdb=" CB TYR R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASN R 72 " pdb=" N ASN R 72 " pdb=" C ASN R 72 " pdb=" CB ASN R 72 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA HIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB HIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1279 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE A 382 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 17 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C GLU G 17 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU G 17 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN G 18 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 381 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ASP A 381 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 381 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 382 " -0.017 2.00e-02 2.50e+03 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1538 2.76 - 3.30: 7675 3.30 - 3.83: 13217 3.83 - 4.37: 16354 4.37 - 4.90: 28407 Nonbonded interactions: 67191 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.230 2.440 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.243 2.520 nonbonded pdb=" OG SER R 116 " pdb=" N PHE R 117 " model vdw 2.252 2.520 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.253 2.520 nonbonded pdb=" OD2 ASP R 122 " pdb=" OH TYR L 2 " model vdw 2.261 2.440 ... (remaining 67186 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=0.20 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: 0.420 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: 1.900 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 26.410 Find NCS groups from input model: 0.180 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.008 0.062 8305 Z= 0.540 Angle : 0.919 8.799 11240 Z= 0.536 Chirality : 0.058 0.287 1282 Planarity : 0.006 0.032 1428 Dihedral : 12.117 139.723 3003 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.08 % Favored : 97.73 % Rotamer: Outliers : 0.45 % Allowed : 3.02 % Favored : 96.53 % 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: 1.14 (0.25), residues: 1014 helix: 1.16 (0.23), residues: 405 sheet: 0.93 (0.34), residues: 225 loop : 0.39 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 99 HIS 0.014 0.003 HIS B 183 PHE 0.050 0.004 PHE N 108 TYR 0.029 0.003 TYR A 339 ARG 0.014 0.002 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 0.977 Fit side-chains REVERT: A 216 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6563 (tptp) REVERT: A 222 PHE cc_start: 0.7425 (m-80) cc_final: 0.7184 (m-80) REVERT: A 381 ASP cc_start: 0.7331 (m-30) cc_final: 0.6983 (m-30) REVERT: B 105 TYR cc_start: 0.8288 (t80) cc_final: 0.8031 (t80) REVERT: B 201 SER cc_start: 0.8908 (t) cc_final: 0.8458 (p) REVERT: B 280 LYS cc_start: 0.8659 (tttt) cc_final: 0.8364 (tttm) REVERT: B 307 VAL cc_start: 0.8620 (m) cc_final: 0.8400 (t) REVERT: N 111 THR cc_start: 0.8550 (p) cc_final: 0.7775 (p) REVERT: R 183 LEU cc_start: 0.8659 (mm) cc_final: 0.8096 (tt) REVERT: R 200 MET cc_start: 0.5299 (mtt) cc_final: 0.5008 (mtp) outliers start: 3 outliers final: 2 residues processed: 241 average time/residue: 1.0604 time to fit residues: 272.2160 Evaluate side-chains 149 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 90 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 390 GLN B 175 GLN B 220 GLN B 266 HIS G 18 GLN R 72 ASN R 76 HIS L 6 HIS A Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8305 Z= 0.177 Angle : 0.546 7.537 11240 Z= 0.298 Chirality : 0.042 0.228 1282 Planarity : 0.004 0.040 1428 Dihedral : 4.794 50.422 1127 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.89 % Favored : 99.01 % Rotamer: Outliers : 4.59 % Allowed : 13.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1014 helix: 2.42 (0.24), residues: 410 sheet: 1.28 (0.33), residues: 220 loop : 0.26 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE B 241 TYR 0.012 0.001 TYR B 289 ARG 0.006 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6967 (ttp-170) cc_final: 0.6718 (mmm160) REVERT: A 216 LYS cc_start: 0.7545 (mmtt) cc_final: 0.6862 (tptp) REVERT: A 314 GLU cc_start: 0.8750 (mm-30) cc_final: 0.7820 (pm20) REVERT: B 46 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7224 (ptm160) REVERT: B 59 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (t80) REVERT: B 105 TYR cc_start: 0.8480 (t80) cc_final: 0.8237 (t80) REVERT: B 201 SER cc_start: 0.8973 (t) cc_final: 0.8690 (p) REVERT: B 280 LYS cc_start: 0.8620 (tttt) cc_final: 0.8419 (tttm) REVERT: G 18 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6824 (tm130) REVERT: G 38 MET cc_start: 0.7946 (ttt) cc_final: 0.7654 (ttm) REVERT: N 109 ASP cc_start: 0.8320 (p0) cc_final: 0.7906 (p0) REVERT: R 316 ILE cc_start: 0.6206 (mt) cc_final: 0.5995 (mp) outliers start: 40 outliers final: 15 residues processed: 189 average time/residue: 1.1192 time to fit residues: 225.0349 Evaluate side-chains 155 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 6 GLN B 175 GLN B 176 GLN N 31 ASN N 77 ASN N 120 GLN R 264 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.169 Angle : 0.498 5.264 11240 Z= 0.273 Chirality : 0.041 0.143 1282 Planarity : 0.004 0.034 1428 Dihedral : 4.552 52.019 1127 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 4.14 % Allowed : 15.88 % Favored : 79.98 % 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: 2.19 (0.26), residues: 1014 helix: 2.70 (0.25), residues: 412 sheet: 1.28 (0.34), residues: 215 loop : 0.22 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE N 108 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 0.886 Fit side-chains REVERT: A 20 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6589 (mmm160) REVERT: A 216 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7171 (tptp) REVERT: B 46 ARG cc_start: 0.7741 (ptm160) cc_final: 0.7342 (ptm160) REVERT: B 59 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8250 (t80) REVERT: B 105 TYR cc_start: 0.8562 (t80) cc_final: 0.8259 (t80) REVERT: B 221 THR cc_start: 0.7677 (m) cc_final: 0.7465 (m) REVERT: B 270 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8798 (pp) REVERT: B 280 LYS cc_start: 0.8670 (tttt) cc_final: 0.8403 (tttm) REVERT: B 301 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8222 (mmmt) REVERT: G 18 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6911 (tm130) REVERT: G 20 LYS cc_start: 0.7870 (pptt) cc_final: 0.7599 (ptpt) REVERT: G 22 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6511 (mt-10) REVERT: G 38 MET cc_start: 0.7923 (ttt) cc_final: 0.7623 (ttm) REVERT: N 82 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7317 (tp40) REVERT: N 120 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: R 189 ASP cc_start: 0.8674 (t0) cc_final: 0.8438 (t70) REVERT: R 286 LEU cc_start: 0.7003 (tt) cc_final: 0.6617 (mp) REVERT: R 309 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7333 (tt) REVERT: R 316 ILE cc_start: 0.6236 (mt) cc_final: 0.5998 (mp) REVERT: L 11 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8756 (mmpt) outliers start: 36 outliers final: 19 residues processed: 174 average time/residue: 0.9506 time to fit residues: 178.1787 Evaluate side-chains 166 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain L residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 6 GLN N 77 ASN R 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8305 Z= 0.204 Angle : 0.499 5.242 11240 Z= 0.275 Chirality : 0.041 0.141 1282 Planarity : 0.004 0.035 1428 Dihedral : 4.293 52.997 1123 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.28 % Favored : 98.62 % Rotamer: Outliers : 5.03 % Allowed : 16.67 % Favored : 78.30 % 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: 2.12 (0.26), residues: 1014 helix: 2.63 (0.24), residues: 419 sheet: 1.14 (0.34), residues: 218 loop : 0.20 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.025 0.002 PHE R 280 TYR 0.013 0.001 TYR B 289 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 0.944 Fit side-chains REVERT: A 216 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7198 (tptp) REVERT: A 314 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7825 (pm20) REVERT: B 44 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 46 ARG cc_start: 0.7788 (ptm160) cc_final: 0.7375 (pmt170) REVERT: B 59 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (t80) REVERT: B 217 MET cc_start: 0.7860 (ptt) cc_final: 0.7273 (pmm) REVERT: B 280 LYS cc_start: 0.8706 (tttt) cc_final: 0.8494 (tttm) REVERT: G 18 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6808 (tm130) REVERT: G 20 LYS cc_start: 0.7883 (pptt) cc_final: 0.7573 (ptpt) REVERT: R 189 ASP cc_start: 0.8631 (t0) cc_final: 0.8389 (t70) REVERT: R 204 MET cc_start: 0.6970 (mpp) cc_final: 0.6740 (tpp) outliers start: 44 outliers final: 22 residues processed: 173 average time/residue: 1.0202 time to fit residues: 189.2225 Evaluate side-chains 166 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 245 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8305 Z= 0.167 Angle : 0.477 6.561 11240 Z= 0.261 Chirality : 0.040 0.138 1282 Planarity : 0.004 0.034 1428 Dihedral : 4.181 53.498 1123 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.03 % Allowed : 18.79 % Favored : 77.18 % 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: 2.18 (0.26), residues: 1014 helix: 2.74 (0.24), residues: 421 sheet: 1.07 (0.33), residues: 221 loop : 0.20 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE N 108 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 0.975 Fit side-chains REVERT: A 20 ARG cc_start: 0.7031 (mmm160) cc_final: 0.6811 (mmm-85) REVERT: A 216 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7227 (tptp) REVERT: B 44 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 46 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7427 (pmt170) REVERT: B 59 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8210 (t80) REVERT: B 217 MET cc_start: 0.7860 (ptt) cc_final: 0.7624 (pmm) REVERT: B 280 LYS cc_start: 0.8745 (tttt) cc_final: 0.8538 (tttm) REVERT: B 307 VAL cc_start: 0.8636 (m) cc_final: 0.8369 (t) REVERT: G 18 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6707 (tm130) REVERT: G 20 LYS cc_start: 0.7889 (pptt) cc_final: 0.7523 (ptpt) REVERT: N 5 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7823 (mm-40) outliers start: 35 outliers final: 23 residues processed: 171 average time/residue: 1.1158 time to fit residues: 204.6002 Evaluate side-chains 165 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 245 ILE Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 292 ASN A 371 ASN B 266 HIS ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8305 Z= 0.186 Angle : 0.481 5.533 11240 Z= 0.263 Chirality : 0.041 0.138 1282 Planarity : 0.004 0.034 1428 Dihedral : 4.168 53.645 1123 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.03 % Allowed : 19.80 % Favored : 76.17 % 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: 2.15 (0.26), residues: 1014 helix: 2.80 (0.24), residues: 419 sheet: 1.00 (0.33), residues: 221 loop : 0.12 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE N 108 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 0.908 Fit side-chains REVERT: A 20 ARG cc_start: 0.7065 (mmm160) cc_final: 0.6848 (mmm-85) REVERT: A 31 GLN cc_start: 0.7011 (mm110) cc_final: 0.6589 (mt0) REVERT: A 216 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7332 (tptp) REVERT: B 44 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: B 46 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7450 (pmt170) REVERT: B 59 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8219 (t80) REVERT: B 217 MET cc_start: 0.7838 (ptt) cc_final: 0.7628 (pmm) REVERT: B 307 VAL cc_start: 0.8622 (m) cc_final: 0.8345 (t) REVERT: G 18 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6662 (tm130) REVERT: G 20 LYS cc_start: 0.7886 (pptt) cc_final: 0.7531 (ptpt) REVERT: N 5 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8018 (mm-40) REVERT: R 204 MET cc_start: 0.6972 (mpp) cc_final: 0.6719 (tpp) REVERT: L 11 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8720 (mmpt) outliers start: 35 outliers final: 23 residues processed: 162 average time/residue: 0.9903 time to fit residues: 171.8968 Evaluate side-chains 159 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 0.0170 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 371 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8305 Z= 0.248 Angle : 0.530 6.436 11240 Z= 0.288 Chirality : 0.042 0.140 1282 Planarity : 0.004 0.042 1428 Dihedral : 4.322 53.860 1123 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.47 % Allowed : 20.02 % Favored : 75.50 % 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: 1.95 (0.26), residues: 1014 helix: 2.70 (0.24), residues: 419 sheet: 0.68 (0.34), residues: 228 loop : 0.09 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS B 183 PHE 0.026 0.002 PHE B 241 TYR 0.013 0.001 TYR N 117 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.015 Fit side-chains REVERT: A 20 ARG cc_start: 0.7021 (mmm160) cc_final: 0.6798 (mmm-85) REVERT: A 31 GLN cc_start: 0.7084 (mm110) cc_final: 0.6598 (mt0) REVERT: A 216 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7301 (tptp) REVERT: A 283 ARG cc_start: 0.6927 (mtt180) cc_final: 0.6602 (mmt90) REVERT: A 299 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: B 44 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: B 46 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7466 (pmt170) REVERT: B 59 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8303 (t80) REVERT: B 127 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7746 (mmtt) REVERT: B 217 MET cc_start: 0.7848 (ptt) cc_final: 0.7628 (pmm) REVERT: B 280 LYS cc_start: 0.8819 (tttt) cc_final: 0.8544 (tttm) REVERT: G 18 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6579 (tm130) REVERT: G 20 LYS cc_start: 0.7886 (pptt) cc_final: 0.7522 (ptpt) REVERT: N 5 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7983 (mm-40) REVERT: R 204 MET cc_start: 0.7051 (mpp) cc_final: 0.6826 (tpp) REVERT: L 11 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8707 (mmpt) outliers start: 39 outliers final: 24 residues processed: 164 average time/residue: 1.0585 time to fit residues: 185.5884 Evaluate side-chains 162 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 245 ILE Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.174 Angle : 0.487 6.628 11240 Z= 0.266 Chirality : 0.041 0.138 1282 Planarity : 0.004 0.036 1428 Dihedral : 4.196 54.104 1123 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.91 % Allowed : 20.58 % Favored : 75.50 % 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: 2.01 (0.26), residues: 1014 helix: 2.76 (0.24), residues: 419 sheet: 0.81 (0.33), residues: 232 loop : -0.00 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.024 0.001 PHE B 241 TYR 0.011 0.001 TYR N 117 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.933 Fit side-chains REVERT: A 20 ARG cc_start: 0.6987 (mmm160) cc_final: 0.6763 (mmm-85) REVERT: A 31 GLN cc_start: 0.6961 (mm110) cc_final: 0.6525 (mt0) REVERT: A 216 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7297 (tptp) REVERT: A 299 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: B 46 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7463 (pmt170) REVERT: B 59 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8271 (t80) REVERT: B 280 LYS cc_start: 0.8770 (tttt) cc_final: 0.8540 (tttm) REVERT: G 18 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6531 (tm130) REVERT: G 20 LYS cc_start: 0.7823 (pptt) cc_final: 0.7470 (ptpt) REVERT: G 62 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6812 (tpm-80) REVERT: N 86 LEU cc_start: 0.8271 (mt) cc_final: 0.8059 (mm) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 0.9983 time to fit residues: 170.4164 Evaluate side-chains 160 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.0060 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 259 GLN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8305 Z= 0.139 Angle : 0.480 6.904 11240 Z= 0.260 Chirality : 0.040 0.139 1282 Planarity : 0.003 0.036 1428 Dihedral : 4.029 54.044 1123 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.80 % Allowed : 22.26 % Favored : 74.94 % 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: 2.06 (0.27), residues: 1014 helix: 2.91 (0.25), residues: 419 sheet: 0.78 (0.33), residues: 225 loop : -0.04 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 339 HIS 0.002 0.000 HIS B 183 PHE 0.011 0.001 PHE A 376 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.905 Fit side-chains REVERT: A 20 ARG cc_start: 0.6945 (mmm160) cc_final: 0.6725 (mmm-85) REVERT: A 216 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7227 (tptp) REVERT: A 299 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: B 46 ARG cc_start: 0.7740 (ptm160) cc_final: 0.7447 (pmt170) REVERT: B 59 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8136 (t80) REVERT: G 20 LYS cc_start: 0.7800 (pptt) cc_final: 0.7392 (ptpt) REVERT: G 62 ARG cc_start: 0.7292 (tpp80) cc_final: 0.6780 (tpm-80) REVERT: N 86 LEU cc_start: 0.8267 (mt) cc_final: 0.7850 (mm) REVERT: L 11 LYS cc_start: 0.8868 (mmpt) cc_final: 0.8559 (mmpt) outliers start: 24 outliers final: 14 residues processed: 160 average time/residue: 1.0276 time to fit residues: 176.2144 Evaluate side-chains 153 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8305 Z= 0.290 Angle : 0.557 9.018 11240 Z= 0.303 Chirality : 0.043 0.175 1282 Planarity : 0.004 0.035 1428 Dihedral : 4.277 54.336 1123 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.24 % Allowed : 22.15 % Favored : 74.61 % 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: 1.85 (0.26), residues: 1014 helix: 2.63 (0.24), residues: 419 sheet: 0.67 (0.33), residues: 236 loop : -0.05 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 339 HIS 0.005 0.001 HIS B 183 PHE 0.027 0.002 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.006 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.026 Fit side-chains REVERT: A 216 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7495 (mmmt) REVERT: A 283 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6550 (mmt90) REVERT: A 299 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: B 44 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: B 46 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7454 (pmt170) REVERT: B 59 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8221 (t80) REVERT: B 280 LYS cc_start: 0.8784 (tttt) cc_final: 0.8570 (tttm) REVERT: G 20 LYS cc_start: 0.7845 (pptt) cc_final: 0.7431 (ptpt) REVERT: G 62 ARG cc_start: 0.7289 (tpp80) cc_final: 0.6809 (tpm-80) REVERT: N 86 LEU cc_start: 0.8403 (mt) cc_final: 0.8018 (mm) REVERT: L 11 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8607 (mmpt) outliers start: 28 outliers final: 18 residues processed: 151 average time/residue: 1.0634 time to fit residues: 171.6282 Evaluate side-chains 152 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 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 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134713 restraints weight = 10436.448| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.90 r_work: 0.3485 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8305 Z= 0.170 Angle : 0.504 8.352 11240 Z= 0.274 Chirality : 0.041 0.138 1282 Planarity : 0.004 0.037 1428 Dihedral : 4.198 54.761 1123 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.24 % Allowed : 23.04 % Favored : 74.72 % 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: 1.92 (0.27), residues: 1014 helix: 2.72 (0.25), residues: 419 sheet: 0.69 (0.33), residues: 236 loop : -0.03 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 339 HIS 0.002 0.001 HIS B 183 PHE 0.015 0.001 PHE R 267 TYR 0.010 0.001 TYR N 117 ARG 0.006 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3472.88 seconds wall clock time: 62 minutes 32.28 seconds (3752.28 seconds total)