Starting phenix.real_space_refine on Sun Aug 4 00:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6o_36925/08_2024/8k6o_36925.cif" } resolution = 3.3 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= 0.002 sd= 0.033 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 68 5.16 5 C 5943 2.51 5 N 1588 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1794 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2444 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 256 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 4, 'TRANS': 25} Chain breaks: 1 Time building chain proxies: 5.46, per 1000 atoms: 0.59 Number of scatterers: 9333 At special positions: 0 Unit cell: (138.55, 121.55, 102.85, 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 68 16.00 O 1734 8.00 N 1588 7.00 C 5943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 38.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.794A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.248A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.947A pdb=" N ALA A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 353 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.724A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 36 through 68 Processing helix chain 'D' and resid 73 through 103 removed outlier: 3.569A pdb=" N ILE D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 109 through 144 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 151 through 176 Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 204 through 220 Processing helix chain 'D' and resid 220 through 249 removed outlier: 3.671A pdb=" N MET D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 288 Proline residue: D 278 - end of helix Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 297 through 321 removed outlier: 3.635A pdb=" N SER D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Proline residue: D 317 - end of helix removed outlier: 3.873A pdb=" N TYR D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 333 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.895A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.525A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'E' and resid 17 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.929A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.547A 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: 6.828A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.952A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.767A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.067A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.993A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.367A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 180 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.665A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.096A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1362 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: 2.55 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3013 1.34 - 1.46: 2103 1.46 - 1.58: 4315 1.58 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9532 Sorted by residual: bond pdb=" CA PHE A 288 " pdb=" CB PHE A 288 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.33e+00 bond pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 1.512 1.522 -0.010 8.70e-03 1.32e+04 1.32e+00 bond pdb=" CA VAL A 202 " pdb=" CB VAL A 202 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.08e-02 8.57e+03 1.26e+00 bond pdb=" CA ILE D 91 " pdb=" C ILE D 91 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.32e-02 5.74e+03 1.07e+00 bond pdb=" CG ARG E 19 " pdb=" CD ARG E 19 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 221 106.78 - 113.57: 5200 113.57 - 120.37: 3466 120.37 - 127.17: 3915 127.17 - 133.96: 105 Bond angle restraints: 12907 Sorted by residual: angle pdb=" C ALA C 45 " pdb=" N LYS C 46 " pdb=" CA LYS C 46 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CG ARG E 19 " pdb=" CD ARG E 19 " pdb=" NE ARG E 19 " ideal model delta sigma weight residual 112.00 118.91 -6.91 2.20e+00 2.07e-01 9.87e+00 angle pdb=" CA MET D 92 " pdb=" CB MET D 92 " pdb=" CG MET D 92 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" N VAL A 202 " pdb=" CA VAL A 202 " pdb=" C VAL A 202 " ideal model delta sigma weight residual 106.42 110.63 -4.21 1.51e+00 4.39e-01 7.78e+00 angle pdb=" CG ARG C 13 " pdb=" CD ARG C 13 " pdb=" NE ARG C 13 " ideal model delta sigma weight residual 112.00 117.80 -5.80 2.20e+00 2.07e-01 6.94e+00 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5108 16.10 - 32.19: 435 32.19 - 48.29: 102 48.29 - 64.38: 19 64.38 - 80.48: 6 Dihedral angle restraints: 5670 sinusoidal: 2225 harmonic: 3445 Sorted by residual: dihedral pdb=" CA MET D 92 " pdb=" C MET D 92 " pdb=" N CYS D 93 " pdb=" CA CYS D 93 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASP D 86 " pdb=" CB ASP D 86 " pdb=" CG ASP D 86 " pdb=" OD1 ASP D 86 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ILE D 91 " pdb=" C ILE D 91 " pdb=" N MET D 92 " pdb=" CA MET D 92 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1242 0.056 - 0.112: 184 0.112 - 0.168: 29 0.168 - 0.224: 0 0.224 - 0.279: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE D 91 " pdb=" CA ILE D 91 " pdb=" CG1 ILE D 91 " pdb=" CG2 ILE D 91 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1453 not shown) Planarity restraints: 1637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.010 2.00e-02 2.50e+03 1.13e-02 3.19e+00 pdb=" CG TRP B 82 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " -0.014 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR S 235 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 222 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO D 223 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.019 5.00e-02 4.00e+02 ... (remaining 1634 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1936 2.78 - 3.31: 8779 3.31 - 3.84: 14846 3.84 - 4.37: 16179 4.37 - 4.90: 29558 Nonbonded interactions: 71298 Sorted by model distance: nonbonded pdb=" NH2 ARG S 87 " pdb=" OE2 GLU S 89 " model vdw 2.255 3.120 nonbonded pdb=" O CYS D 305 " pdb=" OG1 THR D 308 " model vdw 2.278 3.040 nonbonded pdb=" ND2 ASN D 58 " pdb=" OD1 ASP D 86 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASP B 5 " pdb=" NH2 ARG B 8 " model vdw 2.309 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.326 3.040 ... (remaining 71293 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.020 Find NCS groups from input model: 0.110 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 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 0.039 9532 Z= 0.161 Angle : 0.584 7.839 12907 Z= 0.324 Chirality : 0.040 0.279 1456 Planarity : 0.003 0.033 1637 Dihedral : 12.870 80.479 3441 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % 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 (0.24), residues: 1165 helix: 3.10 (0.25), residues: 421 sheet: 1.50 (0.31), residues: 280 loop : -0.50 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 82 HIS 0.003 0.001 HIS A 281 PHE 0.017 0.001 PHE B 199 TYR 0.022 0.001 TYR S 235 ARG 0.006 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.972 Fit side-chains REVERT: A 53 MET cc_start: 0.4794 (mmm) cc_final: 0.4445 (mmm) REVERT: B 124 TYR cc_start: 0.7444 (m-80) cc_final: 0.7208 (m-80) REVERT: B 245 SER cc_start: 0.7354 (t) cc_final: 0.6379 (t) REVERT: B 246 ASP cc_start: 0.7126 (m-30) cc_final: 0.6728 (m-30) REVERT: B 312 ASP cc_start: 0.7160 (p0) cc_final: 0.6811 (p0) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2028 time to fit residues: 53.5112 Evaluate side-chains 155 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 91 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 256 ASN B 75 GLN B 110 ASN D 177 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9532 Z= 0.176 Angle : 0.541 7.112 12907 Z= 0.289 Chirality : 0.041 0.160 1456 Planarity : 0.004 0.039 1637 Dihedral : 3.958 24.388 1281 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 8.10 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1165 helix: 3.09 (0.24), residues: 435 sheet: 1.36 (0.31), residues: 287 loop : -0.58 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.001 PHE S 177 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.119 Fit side-chains REVERT: A 241 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.5222 (pmm) REVERT: B 55 LEU cc_start: 0.7281 (mt) cc_final: 0.7009 (mp) REVERT: B 124 TYR cc_start: 0.7764 (m-80) cc_final: 0.7563 (m-80) REVERT: B 290 ASP cc_start: 0.6393 (m-30) cc_final: 0.6074 (m-30) outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 0.2231 time to fit residues: 53.0292 Evaluate side-chains 158 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.0270 chunk 94 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN D 306 HIS S 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9532 Z= 0.159 Angle : 0.511 6.284 12907 Z= 0.273 Chirality : 0.040 0.150 1456 Planarity : 0.004 0.044 1637 Dihedral : 3.943 22.971 1281 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.46 % Allowed : 11.80 % Favored : 86.73 % 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: 2.00 (0.24), residues: 1165 helix: 3.19 (0.24), residues: 434 sheet: 1.42 (0.31), residues: 280 loop : -0.68 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.010 0.001 HIS D 306 PHE 0.021 0.001 PHE D 184 TYR 0.020 0.001 TYR S 235 ARG 0.005 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 0.992 Fit side-chains REVERT: A 190 PHE cc_start: 0.8210 (p90) cc_final: 0.7969 (p90) REVERT: A 191 THR cc_start: 0.8268 (p) cc_final: 0.8031 (m) REVERT: A 241 MET cc_start: 0.5356 (pmm) cc_final: 0.4672 (pmm) REVERT: A 244 MET cc_start: 0.8000 (tpp) cc_final: 0.7360 (tpp) REVERT: B 55 LEU cc_start: 0.7393 (mt) cc_final: 0.7127 (mp) REVERT: B 110 ASN cc_start: 0.7542 (m-40) cc_final: 0.7198 (m110) REVERT: B 259 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5391 (mm-40) REVERT: B 304 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: C 50 LEU cc_start: 0.8435 (mm) cc_final: 0.8139 (mm) REVERT: D 226 PHE cc_start: 0.6750 (t80) cc_final: 0.6529 (t80) REVERT: D 233 LYS cc_start: 0.7894 (ttmm) cc_final: 0.7560 (mtpp) outliers start: 15 outliers final: 6 residues processed: 164 average time/residue: 0.2145 time to fit residues: 48.6203 Evaluate side-chains 157 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 234 ILE 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: 0.6980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9532 Z= 0.243 Angle : 0.594 10.247 12907 Z= 0.318 Chirality : 0.043 0.194 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.338 22.567 1281 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.76 % Allowed : 14.34 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.24), residues: 1165 helix: 3.06 (0.24), residues: 426 sheet: 1.15 (0.31), residues: 290 loop : -0.83 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 36 HIS 0.008 0.002 HIS B 225 PHE 0.022 0.002 PHE D 184 TYR 0.027 0.002 TYR S 235 ARG 0.005 0.001 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 0.993 Fit side-chains REVERT: A 262 ASP cc_start: 0.6810 (p0) cc_final: 0.6355 (p0) REVERT: B 55 LEU cc_start: 0.7423 (mt) cc_final: 0.7179 (mp) REVERT: B 76 ASP cc_start: 0.6655 (t0) cc_final: 0.6444 (t0) REVERT: B 110 ASN cc_start: 0.7814 (m-40) cc_final: 0.7472 (m110) REVERT: C 21 MET cc_start: 0.6063 (tmm) cc_final: 0.5601 (tmm) REVERT: C 50 LEU cc_start: 0.8394 (mm) cc_final: 0.8187 (mt) REVERT: D 310 MET cc_start: 0.6938 (tpp) cc_final: 0.6548 (mmm) outliers start: 18 outliers final: 8 residues processed: 167 average time/residue: 0.2193 time to fit residues: 50.3433 Evaluate side-chains 157 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 245 HIS C 59 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9532 Z= 0.201 Angle : 0.541 8.314 12907 Z= 0.289 Chirality : 0.041 0.171 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.179 23.059 1281 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.24 % Allowed : 16.49 % Favored : 81.27 % 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: 1.68 (0.25), residues: 1165 helix: 3.16 (0.24), residues: 426 sheet: 0.92 (0.30), residues: 299 loop : -0.88 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.005 0.001 HIS B 54 PHE 0.022 0.002 PHE D 184 TYR 0.028 0.002 TYR S 235 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 0.999 Fit side-chains REVERT: A 241 MET cc_start: 0.5253 (pmm) cc_final: 0.4294 (pmm) REVERT: B 76 ASP cc_start: 0.6680 (t0) cc_final: 0.6388 (t0) REVERT: C 21 MET cc_start: 0.6088 (tmm) cc_final: 0.5644 (tmm) REVERT: C 38 MET cc_start: 0.7906 (ttt) cc_final: 0.7691 (ttp) REVERT: D 310 MET cc_start: 0.7083 (tpp) cc_final: 0.6644 (mmm) outliers start: 23 outliers final: 17 residues processed: 172 average time/residue: 0.2269 time to fit residues: 53.1489 Evaluate side-chains 170 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 18 GLN C 59 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9532 Z= 0.264 Angle : 0.586 8.566 12907 Z= 0.316 Chirality : 0.043 0.195 1456 Planarity : 0.004 0.050 1637 Dihedral : 4.407 22.309 1281 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.93 % Allowed : 17.27 % Favored : 79.80 % 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: 1.50 (0.25), residues: 1165 helix: 3.01 (0.24), residues: 427 sheet: 0.87 (0.30), residues: 293 loop : -1.02 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 163 HIS 0.007 0.001 HIS B 225 PHE 0.023 0.002 PHE D 184 TYR 0.032 0.002 TYR S 235 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.013 Fit side-chains REVERT: A 191 THR cc_start: 0.8749 (p) cc_final: 0.8409 (t) REVERT: A 241 MET cc_start: 0.5365 (pmm) cc_final: 0.4390 (pmm) REVERT: B 76 ASP cc_start: 0.6702 (t0) cc_final: 0.6489 (t0) REVERT: B 110 ASN cc_start: 0.7725 (m-40) cc_final: 0.7382 (m110) REVERT: C 59 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7899 (t0) REVERT: D 233 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7582 (mtpp) REVERT: D 310 MET cc_start: 0.7177 (tpp) cc_final: 0.6916 (mmm) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 0.2231 time to fit residues: 58.0128 Evaluate side-chains 194 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.0370 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9532 Z= 0.154 Angle : 0.537 9.644 12907 Z= 0.284 Chirality : 0.041 0.167 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.235 27.255 1281 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.44 % Allowed : 19.80 % Favored : 77.76 % 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: 1.60 (0.25), residues: 1165 helix: 3.17 (0.24), residues: 427 sheet: 0.86 (0.30), residues: 288 loop : -0.98 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS D 139 PHE 0.025 0.001 PHE D 184 TYR 0.028 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 191 THR cc_start: 0.8709 (p) cc_final: 0.8368 (t) REVERT: A 241 MET cc_start: 0.5175 (pmm) cc_final: 0.4302 (pmm) REVERT: B 110 ASN cc_start: 0.7676 (m-40) cc_final: 0.7396 (m110) REVERT: B 290 ASP cc_start: 0.6227 (m-30) cc_final: 0.5713 (m-30) REVERT: D 310 MET cc_start: 0.7084 (tpp) cc_final: 0.6766 (mmm) outliers start: 25 outliers final: 21 residues processed: 176 average time/residue: 0.2259 time to fit residues: 54.0809 Evaluate side-chains 184 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9532 Z= 0.146 Angle : 0.539 10.265 12907 Z= 0.281 Chirality : 0.040 0.174 1456 Planarity : 0.004 0.046 1637 Dihedral : 4.144 28.940 1281 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.76 % Allowed : 21.17 % Favored : 77.07 % 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: 1.63 (0.25), residues: 1165 helix: 3.28 (0.24), residues: 427 sheet: 0.86 (0.31), residues: 277 loop : -0.99 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.003 0.001 HIS D 139 PHE 0.025 0.001 PHE D 184 TYR 0.026 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.5072 (pmm) cc_final: 0.4328 (pmm) REVERT: A 307 LYS cc_start: 0.6910 (mtpt) cc_final: 0.6654 (mtpt) REVERT: B 290 ASP cc_start: 0.6215 (m-30) cc_final: 0.5748 (m-30) REVERT: D 88 LEU cc_start: 0.7360 (tp) cc_final: 0.7156 (tt) outliers start: 18 outliers final: 15 residues processed: 175 average time/residue: 0.2323 time to fit residues: 55.0114 Evaluate side-chains 178 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9532 Z= 0.260 Angle : 0.621 9.624 12907 Z= 0.327 Chirality : 0.043 0.221 1456 Planarity : 0.004 0.045 1637 Dihedral : 4.410 24.704 1281 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 21.37 % Favored : 76.39 % 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: 1.41 (0.25), residues: 1165 helix: 3.05 (0.24), residues: 427 sheet: 0.80 (0.30), residues: 288 loop : -1.16 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 148 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.002 PHE D 184 TYR 0.037 0.002 TYR S 235 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.5173 (pmm) cc_final: 0.4661 (pmm) REVERT: A 307 LYS cc_start: 0.6885 (mtpt) cc_final: 0.6480 (mtpt) REVERT: B 70 LEU cc_start: 0.6980 (tp) cc_final: 0.6742 (mt) REVERT: B 247 ASP cc_start: 0.7252 (p0) cc_final: 0.6970 (p0) REVERT: D 310 MET cc_start: 0.7340 (mmm) cc_final: 0.7045 (mmt) outliers start: 23 outliers final: 18 residues processed: 192 average time/residue: 0.2210 time to fit residues: 58.3599 Evaluate side-chains 187 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9532 Z= 0.230 Angle : 0.603 9.327 12907 Z= 0.316 Chirality : 0.043 0.256 1456 Planarity : 0.004 0.060 1637 Dihedral : 4.401 26.526 1281 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.66 % Allowed : 22.83 % Favored : 75.51 % 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: 1.38 (0.25), residues: 1165 helix: 3.01 (0.24), residues: 427 sheet: 0.82 (0.30), residues: 295 loop : -1.22 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 148 HIS 0.005 0.001 HIS B 54 PHE 0.028 0.002 PHE D 184 TYR 0.032 0.002 TYR S 235 ARG 0.009 0.000 ARG D 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 233 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 241 MET cc_start: 0.5106 (pmm) cc_final: 0.4365 (pmm) REVERT: A 307 LYS cc_start: 0.6914 (mtpt) cc_final: 0.6479 (mtpt) REVERT: B 247 ASP cc_start: 0.7269 (p0) cc_final: 0.6970 (p0) REVERT: C 50 LEU cc_start: 0.8188 (mm) cc_final: 0.7912 (mt) REVERT: S 96 CYS cc_start: 0.6610 (t) cc_final: 0.6353 (t) outliers start: 17 outliers final: 16 residues processed: 186 average time/residue: 0.2118 time to fit residues: 54.6270 Evaluate side-chains 189 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125995 restraints weight = 13125.180| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.29 r_work: 0.3474 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9532 Z= 0.165 Angle : 0.571 9.445 12907 Z= 0.297 Chirality : 0.041 0.226 1456 Planarity : 0.004 0.045 1637 Dihedral : 4.235 29.646 1281 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.76 % Allowed : 22.73 % Favored : 75.51 % 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: 1.57 (0.25), residues: 1165 helix: 3.29 (0.24), residues: 421 sheet: 0.87 (0.30), residues: 295 loop : -1.16 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 63 HIS 0.002 0.001 HIS D 306 PHE 0.028 0.001 PHE D 184 TYR 0.027 0.001 TYR S 235 ARG 0.008 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.22 seconds wall clock time: 44 minutes 15.30 seconds (2655.30 seconds total)