Starting phenix.real_space_refine on Wed Feb 14 14:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdx_23783/02_2024/7mdx_23783_updated.pdb" } resolution = 3.8 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= 0.054 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 52 5.16 5 C 6065 2.51 5 N 1664 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2980 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 21, 'TRANS': 371} Chain: "B" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3112 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1668 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1668 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'YPC': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'COO': 1, 'PEPT-D': 3} Link IDs: {'CIS': 2, 'TRANS': 2, None: 1} Not linked: pdbres="YPC E 1 " pdbres="DSN E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'YPC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.10, per 1000 atoms: 0.54 Number of scatterers: 9513 At special positions: 0 Unit cell: (94.34, 72.08, 155.82, 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 52 16.00 O 1732 8.00 N 1664 7.00 C 6065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN E 2 " pdb=" CB DAL E 3 " pdb=" CB DAL E 4 " Number of C-beta restraints generated: 2254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 41.4% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 29 through 59 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 229 through 236 removed outlier: 4.698A pdb=" N ASP A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 291 removed outlier: 3.837A pdb=" N THR A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.527A pdb=" N THR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 340 removed outlier: 3.516A pdb=" N MET A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 387 removed outlier: 3.543A pdb=" N THR A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Proline residue: A 383 - end of helix Processing helix chain 'B' and resid 7 through 16 Processing helix chain 'B' and resid 23 through 26 No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 28 through 58 Processing helix chain 'B' and resid 83 through 86 No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.589A pdb=" N GLN B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.765A pdb=" N LEU B 237 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 No H-bonds generated for 'chain 'B' and resid 254 through 257' Processing helix chain 'B' and resid 259 through 307 removed outlier: 3.605A pdb=" N ARG B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 342 removed outlier: 3.594A pdb=" N ARG B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 379 through 402 removed outlier: 4.444A pdb=" N TYR B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Proline residue: B 398 - end of helix Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 78 through 87 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 119 through 133 removed outlier: 4.026A pdb=" N ASN D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 128 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.910A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 4.785A pdb=" N PHE D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.276A pdb=" N HIS C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.786A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 119 through 133 removed outlier: 3.528A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 4.074A pdb=" N GLN C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.657A pdb=" N ILE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 188 " --> pdb=" O PHE C 185 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.697A pdb=" N GLN A 247 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 69 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.676A pdb=" N GLY A 221 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.612A pdb=" N SER A 180 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 166 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A 182 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 164 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 163 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 99 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.090A pdb=" N ALA B 204 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.675A pdb=" N VAL B 104 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 111 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 109 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.420A pdb=" N LEU D 166 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU D 200 " --> pdb=" O ALA D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 339 hydrogen bonds defined for protein. 942 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: 2.06 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1581 1.31 - 1.44: 2328 1.44 - 1.56: 5664 1.56 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 9671 Sorted by residual: bond pdb=" C DSN E 2 " pdb=" N DAL E 3 " ideal model delta sigma weight residual 1.329 1.458 -0.129 1.40e-02 5.10e+03 8.50e+01 bond pdb=" C DAL E 3 " pdb=" N DAL E 4 " ideal model delta sigma weight residual 1.329 1.453 -0.124 1.40e-02 5.10e+03 7.87e+01 bond pdb=" C DAL E 4 " pdb=" N ALA E 5 " ideal model delta sigma weight residual 1.329 1.452 -0.123 1.40e-02 5.10e+03 7.71e+01 bond pdb=" C ALA E 5 " pdb=" N ALA E 6 " ideal model delta sigma weight residual 1.329 1.451 -0.122 1.40e-02 5.10e+03 7.62e+01 bond pdb=" C57 YPC E 1 " pdb=" O58 YPC E 1 " ideal model delta sigma weight residual 1.259 1.184 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 9666 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.50: 198 105.50 - 112.65: 5170 112.65 - 119.81: 3175 119.81 - 126.97: 4437 126.97 - 134.12: 106 Bond angle restraints: 13086 Sorted by residual: angle pdb=" N VAL A 5 " pdb=" CA VAL A 5 " pdb=" C VAL A 5 " ideal model delta sigma weight residual 113.20 108.90 4.30 9.60e-01 1.09e+00 2.01e+01 angle pdb=" N ILE B 59 " pdb=" CA ILE B 59 " pdb=" C ILE B 59 " ideal model delta sigma weight residual 111.62 108.76 2.86 7.90e-01 1.60e+00 1.31e+01 angle pdb=" C ASN B 77 " pdb=" N TRP B 78 " pdb=" CA TRP B 78 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CA DSN E 2 " pdb=" C DSN E 2 " pdb=" N DAL E 3 " ideal model delta sigma weight residual 116.20 123.13 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N DAL E 3 " pdb=" CA DAL E 3 " pdb=" CB DAL E 3 " ideal model delta sigma weight residual 110.40 114.87 -4.47 1.50e+00 4.44e-01 8.87e+00 ... (remaining 13081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 5713 34.59 - 69.17: 123 69.17 - 103.76: 19 103.76 - 138.34: 2 138.34 - 172.93: 2 Dihedral angle restraints: 5859 sinusoidal: 2350 harmonic: 3509 Sorted by residual: dihedral pdb=" C27 YPC E 1 " pdb=" C28 YPC E 1 " pdb=" C29 YPC E 1 " pdb=" C30 YPC E 1 " ideal model delta sinusoidal sigma weight residual 172.89 -0.04 172.93 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C31 YPC E 1 " pdb=" C32 YPC E 1 " pdb=" C33 YPC E 1 " pdb=" C34 YPC E 1 " ideal model delta sinusoidal sigma weight residual 190.34 29.88 160.46 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA MET A 291 " pdb=" C MET A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 5856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1473 0.101 - 0.202: 43 0.202 - 0.303: 0 0.303 - 0.404: 3 0.404 - 0.506: 2 Chirality restraints: 1521 Sorted by residual: chirality pdb=" C39 YPC E 1 " pdb=" C38 YPC E 1 " pdb=" C57 YPC E 1 " pdb=" N40 YPC E 1 " both_signs ideal model delta sigma weight residual False 2.61 2.10 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA ALA E 5 " pdb=" N ALA E 5 " pdb=" C ALA E 5 " pdb=" CB ALA E 5 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA DSN E 2 " pdb=" N DSN E 2 " pdb=" C DSN E 2 " pdb=" CB DSN E 2 " both_signs ideal model delta sigma weight residual False -2.51 -2.12 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1518 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 3 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO A 4 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 118 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO D 119 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 371 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 372 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " 0.027 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1496 2.76 - 3.30: 9823 3.30 - 3.83: 14859 3.83 - 4.37: 16985 4.37 - 4.90: 28285 Nonbonded interactions: 71448 Sorted by model distance: nonbonded pdb=" O GLU C 217 " pdb=" NH1 ARG C 219 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS A 293 " pdb=" OD2 ASP C 101 " model vdw 2.275 2.520 nonbonded pdb=" OD1 ASN B 56 " pdb=" OH TYR B 262 " model vdw 2.295 2.440 nonbonded pdb=" NH1 ARG B 306 " pdb=" OD1 ASP B 312 " model vdw 2.303 2.520 nonbonded pdb=" O LEU D 51 " pdb=" N LEU D 55 " model vdw 2.309 2.520 ... (remaining 71443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.030 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.430 Find NCS groups from input model: 0.340 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.004 0.129 9671 Z= 0.256 Angle : 0.702 9.609 13086 Z= 0.360 Chirality : 0.048 0.506 1521 Planarity : 0.005 0.123 1683 Dihedral : 15.650 172.926 3605 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.61 % Cbeta Deviations : 0.09 % 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: -1.27 (0.24), residues: 1224 helix: 0.85 (0.24), residues: 500 sheet: -2.11 (0.58), residues: 69 loop : -2.16 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 254 HIS 0.005 0.001 HIS C 97 PHE 0.021 0.001 PHE D 30 TYR 0.019 0.001 TYR D 93 ARG 0.014 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8427 (tpp) cc_final: 0.8093 (tpp) REVERT: A 121 GLN cc_start: 0.8523 (mp10) cc_final: 0.8288 (mp10) REVERT: A 148 GLU cc_start: 0.8215 (tt0) cc_final: 0.7865 (tt0) REVERT: A 213 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8376 (mtt180) REVERT: A 246 TRP cc_start: 0.8661 (t-100) cc_final: 0.8453 (t-100) REVERT: A 296 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 136 ASP cc_start: 0.7952 (m-30) cc_final: 0.7704 (m-30) REVERT: B 169 MET cc_start: 0.7402 (ttp) cc_final: 0.6895 (ttp) REVERT: B 215 LEU cc_start: 0.8806 (tt) cc_final: 0.8277 (tt) REVERT: B 246 ASN cc_start: 0.7065 (m110) cc_final: 0.6828 (m110) REVERT: B 267 MET cc_start: 0.8446 (ttp) cc_final: 0.8167 (ttt) REVERT: B 314 LEU cc_start: 0.8533 (tp) cc_final: 0.8307 (tt) REVERT: B 348 ILE cc_start: 0.8838 (pt) cc_final: 0.8628 (pt) REVERT: B 378 LEU cc_start: 0.8948 (tp) cc_final: 0.8718 (tp) REVERT: D 38 MET cc_start: 0.3774 (mtm) cc_final: 0.3044 (mpp) REVERT: D 84 LEU cc_start: 0.8619 (mt) cc_final: 0.8409 (mt) REVERT: D 129 MET cc_start: 0.9254 (mmm) cc_final: 0.8987 (mmm) REVERT: D 141 HIS cc_start: 0.7955 (p90) cc_final: 0.7746 (p90) REVERT: D 180 ASN cc_start: 0.8160 (m110) cc_final: 0.7940 (m110) REVERT: C 38 MET cc_start: 0.6821 (mtm) cc_final: 0.6541 (mtt) REVERT: C 92 ILE cc_start: 0.8220 (pt) cc_final: 0.7996 (pt) REVERT: C 99 LEU cc_start: 0.8699 (tp) cc_final: 0.7859 (tp) REVERT: C 125 ARG cc_start: 0.7303 (ptp-110) cc_final: 0.7046 (ptp-170) REVERT: C 141 HIS cc_start: 0.8799 (m170) cc_final: 0.8510 (m170) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.1891 time to fit residues: 94.9464 Evaluate side-chains 331 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 294 GLN B 57 ASN B 212 GLN B 233 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9671 Z= 0.189 Angle : 0.629 7.047 13086 Z= 0.311 Chirality : 0.044 0.205 1521 Planarity : 0.005 0.086 1683 Dihedral : 9.574 111.735 1373 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 2.86 % Allowed : 13.92 % Favored : 83.22 % 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: -1.17 (0.24), residues: 1224 helix: 0.98 (0.23), residues: 512 sheet: -1.55 (0.60), residues: 77 loop : -2.28 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.004 0.001 HIS C 97 PHE 0.022 0.001 PHE B 100 TYR 0.023 0.001 TYR D 93 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 336 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8573 (tp30) cc_final: 0.8369 (tp30) REVERT: A 121 GLN cc_start: 0.8566 (mp10) cc_final: 0.8297 (mp10) REVERT: A 148 GLU cc_start: 0.8294 (tt0) cc_final: 0.7915 (tt0) REVERT: A 195 GLU cc_start: 0.8773 (pp20) cc_final: 0.8563 (pp20) REVERT: A 213 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8382 (mtt180) REVERT: A 317 GLN cc_start: 0.8583 (tp40) cc_final: 0.8254 (tp40) REVERT: B 136 ASP cc_start: 0.8010 (m-30) cc_final: 0.7713 (m-30) REVERT: B 169 MET cc_start: 0.7545 (ttp) cc_final: 0.7047 (ttp) REVERT: B 180 MET cc_start: 0.7339 (mpp) cc_final: 0.7024 (mpp) REVERT: B 246 ASN cc_start: 0.6997 (m110) cc_final: 0.6706 (m110) REVERT: B 267 MET cc_start: 0.8432 (ttp) cc_final: 0.8071 (ttm) REVERT: B 293 MET cc_start: 0.8726 (tmm) cc_final: 0.7759 (tpt) REVERT: B 314 LEU cc_start: 0.8895 (tp) cc_final: 0.8616 (tt) REVERT: B 348 ILE cc_start: 0.8834 (pt) cc_final: 0.8616 (pt) REVERT: B 356 ILE cc_start: 0.8952 (tt) cc_final: 0.8687 (tt) REVERT: D 38 MET cc_start: 0.4064 (mtm) cc_final: 0.3340 (mpp) REVERT: D 86 ASN cc_start: 0.9329 (t0) cc_final: 0.9066 (t0) REVERT: D 121 GLU cc_start: 0.8755 (mp0) cc_final: 0.8370 (mp0) REVERT: C 38 MET cc_start: 0.6997 (mtm) cc_final: 0.6464 (mtt) REVERT: C 97 HIS cc_start: 0.7512 (m170) cc_final: 0.7152 (m170) REVERT: C 129 MET cc_start: 0.7142 (ttt) cc_final: 0.6778 (mtt) REVERT: C 141 HIS cc_start: 0.8779 (m170) cc_final: 0.8478 (m170) outliers start: 29 outliers final: 22 residues processed: 341 average time/residue: 0.1840 time to fit residues: 89.7002 Evaluate side-chains 352 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 330 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN B 57 ASN B 212 GLN B 233 ASN B 246 ASN D 86 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9671 Z= 0.240 Angle : 0.648 8.517 13086 Z= 0.320 Chirality : 0.044 0.221 1521 Planarity : 0.004 0.068 1683 Dihedral : 8.292 90.897 1371 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.48 % Favored : 90.44 % Rotamer: Outliers : 4.64 % Allowed : 17.97 % Favored : 77.39 % 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: -1.34 (0.24), residues: 1224 helix: 0.79 (0.23), residues: 508 sheet: -2.11 (0.56), residues: 80 loop : -2.23 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 246 HIS 0.004 0.001 HIS D 97 PHE 0.018 0.002 PHE D 95 TYR 0.017 0.001 TYR D 93 ARG 0.004 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 351 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8793 (m-80) cc_final: 0.8591 (m-80) REVERT: A 53 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8071 (ttp80) REVERT: A 121 GLN cc_start: 0.8627 (mp10) cc_final: 0.8315 (mp10) REVERT: A 148 GLU cc_start: 0.8287 (tt0) cc_final: 0.7882 (tt0) REVERT: A 317 GLN cc_start: 0.8619 (tp40) cc_final: 0.8368 (tp40) REVERT: B 136 ASP cc_start: 0.8026 (m-30) cc_final: 0.7732 (m-30) REVERT: B 169 MET cc_start: 0.7649 (ttp) cc_final: 0.7202 (ttp) REVERT: B 180 MET cc_start: 0.7902 (mpp) cc_final: 0.7419 (mpp) REVERT: B 246 ASN cc_start: 0.6768 (m-40) cc_final: 0.6406 (m110) REVERT: B 267 MET cc_start: 0.8524 (ttp) cc_final: 0.8215 (ttm) REVERT: B 293 MET cc_start: 0.8700 (tmm) cc_final: 0.7796 (tpt) REVERT: B 314 LEU cc_start: 0.9025 (tp) cc_final: 0.8771 (tt) REVERT: B 356 ILE cc_start: 0.9017 (tt) cc_final: 0.8786 (tt) REVERT: D 137 HIS cc_start: 0.7483 (m-70) cc_final: 0.7280 (p-80) REVERT: D 197 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6171 (t) REVERT: C 38 MET cc_start: 0.7073 (mtm) cc_final: 0.6516 (mtt) REVERT: C 97 HIS cc_start: 0.7732 (m170) cc_final: 0.7208 (m170) REVERT: C 129 MET cc_start: 0.7387 (ttt) cc_final: 0.7026 (mtt) REVERT: C 141 HIS cc_start: 0.8839 (m170) cc_final: 0.8446 (m90) outliers start: 47 outliers final: 40 residues processed: 360 average time/residue: 0.1823 time to fit residues: 92.9935 Evaluate side-chains 383 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 342 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 57 ASN B 233 ASN B 359 GLN D 86 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9671 Z= 0.197 Angle : 0.625 7.595 13086 Z= 0.306 Chirality : 0.043 0.236 1521 Planarity : 0.004 0.057 1683 Dihedral : 8.053 87.947 1371 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.82 % Favored : 91.09 % Rotamer: Outliers : 4.94 % Allowed : 21.13 % Favored : 73.94 % 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: -1.27 (0.24), residues: 1224 helix: 0.91 (0.23), residues: 507 sheet: -2.42 (0.57), residues: 73 loop : -2.21 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 254 HIS 0.003 0.000 HIS D 97 PHE 0.016 0.001 PHE D 95 TYR 0.008 0.001 TYR A 199 ARG 0.009 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 337 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8218 (tm-30) REVERT: A 92 ARG cc_start: 0.8358 (ptt90) cc_final: 0.8042 (ppt170) REVERT: A 121 GLN cc_start: 0.8593 (mp10) cc_final: 0.8297 (mp10) REVERT: A 148 GLU cc_start: 0.8276 (tt0) cc_final: 0.7872 (tt0) REVERT: A 210 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8070 (mmm-85) REVERT: A 317 GLN cc_start: 0.8728 (tp40) cc_final: 0.8295 (tp40) REVERT: B 136 ASP cc_start: 0.8069 (m-30) cc_final: 0.7806 (m-30) REVERT: B 169 MET cc_start: 0.7544 (ttp) cc_final: 0.7024 (ttp) REVERT: B 180 MET cc_start: 0.7905 (mpp) cc_final: 0.7561 (mpp) REVERT: B 212 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8832 (mm-40) REVERT: B 267 MET cc_start: 0.8497 (ttp) cc_final: 0.8192 (ttm) REVERT: B 293 MET cc_start: 0.8628 (tmm) cc_final: 0.7761 (tpt) REVERT: B 356 ILE cc_start: 0.9098 (tt) cc_final: 0.8889 (tt) REVERT: D 197 THR cc_start: 0.6386 (OUTLIER) cc_final: 0.6011 (t) REVERT: C 38 MET cc_start: 0.7035 (mtm) cc_final: 0.6570 (mtt) REVERT: C 55 LEU cc_start: 0.9543 (mm) cc_final: 0.9338 (mm) REVERT: C 97 HIS cc_start: 0.7750 (m170) cc_final: 0.7179 (m170) REVERT: C 141 HIS cc_start: 0.8840 (m170) cc_final: 0.8448 (m90) outliers start: 50 outliers final: 39 residues processed: 353 average time/residue: 0.1929 time to fit residues: 96.9250 Evaluate side-chains 373 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 333 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 233 ASN B 246 ASN D 162 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9671 Z= 0.261 Angle : 0.659 8.671 13086 Z= 0.326 Chirality : 0.044 0.235 1521 Planarity : 0.004 0.047 1683 Dihedral : 7.876 87.865 1371 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.72 % Favored : 90.20 % Rotamer: Outliers : 5.82 % Allowed : 22.51 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.24), residues: 1224 helix: 0.80 (0.23), residues: 505 sheet: -2.13 (0.56), residues: 85 loop : -2.23 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 246 HIS 0.003 0.001 HIS D 97 PHE 0.018 0.002 PHE A 257 TYR 0.011 0.001 TYR D 93 ARG 0.010 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 346 time to evaluate : 1.207 Fit side-chains REVERT: A 82 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 114 MET cc_start: 0.9069 (ptt) cc_final: 0.8850 (ptm) REVERT: A 118 ASP cc_start: 0.8117 (t0) cc_final: 0.7068 (t0) REVERT: A 121 GLN cc_start: 0.8604 (mp10) cc_final: 0.8023 (mp10) REVERT: A 148 GLU cc_start: 0.8318 (tt0) cc_final: 0.8012 (tt0) REVERT: A 200 GLU cc_start: 0.8791 (tp30) cc_final: 0.8356 (tp30) REVERT: A 210 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8042 (mmm-85) REVERT: A 317 GLN cc_start: 0.8842 (tp40) cc_final: 0.8372 (tp40) REVERT: B 136 ASP cc_start: 0.8124 (m-30) cc_final: 0.7812 (m-30) REVERT: B 169 MET cc_start: 0.7608 (ttp) cc_final: 0.7163 (ttp) REVERT: B 212 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8772 (mm-40) REVERT: B 232 PHE cc_start: 0.8218 (m-80) cc_final: 0.8007 (m-80) REVERT: B 258 TYR cc_start: 0.9203 (m-80) cc_final: 0.8096 (m-80) REVERT: B 267 MET cc_start: 0.8538 (ttp) cc_final: 0.8212 (ttm) REVERT: B 293 MET cc_start: 0.8641 (tmm) cc_final: 0.7714 (tpt) REVERT: B 356 ILE cc_start: 0.9107 (tt) cc_final: 0.8906 (tt) REVERT: D 86 ASN cc_start: 0.9238 (t0) cc_final: 0.8947 (t0) REVERT: C 38 MET cc_start: 0.7017 (mtm) cc_final: 0.6492 (mtt) REVERT: C 55 LEU cc_start: 0.9560 (mm) cc_final: 0.9337 (mm) REVERT: C 97 HIS cc_start: 0.7877 (m170) cc_final: 0.7205 (m170) REVERT: C 141 HIS cc_start: 0.8842 (m170) cc_final: 0.8411 (m170) outliers start: 59 outliers final: 50 residues processed: 365 average time/residue: 0.1877 time to fit residues: 98.0060 Evaluate side-chains 391 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 341 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 57 ASN B 57 ASN B 233 ASN B 246 ASN D 162 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9671 Z= 0.199 Angle : 0.654 9.183 13086 Z= 0.315 Chirality : 0.043 0.250 1521 Planarity : 0.004 0.044 1683 Dihedral : 7.611 90.670 1371 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.74 % Favored : 91.18 % Rotamer: Outliers : 5.03 % Allowed : 25.27 % Favored : 69.69 % 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: -1.36 (0.24), residues: 1224 helix: 0.83 (0.23), residues: 514 sheet: -2.29 (0.58), residues: 73 loop : -2.31 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 254 HIS 0.003 0.001 HIS D 97 PHE 0.015 0.001 PHE A 257 TYR 0.015 0.001 TYR B 97 ARG 0.010 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 340 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8310 (tpp) cc_final: 0.7690 (mmp) REVERT: A 39 MET cc_start: 0.8608 (tpp) cc_final: 0.8341 (tpp) REVERT: A 82 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 114 MET cc_start: 0.9067 (ptt) cc_final: 0.8856 (ptm) REVERT: A 118 ASP cc_start: 0.8046 (t0) cc_final: 0.7022 (t0) REVERT: A 121 GLN cc_start: 0.8584 (mp10) cc_final: 0.8019 (mp10) REVERT: A 148 GLU cc_start: 0.8374 (tt0) cc_final: 0.7980 (tt0) REVERT: A 195 GLU cc_start: 0.8808 (pp20) cc_final: 0.8161 (pp20) REVERT: A 199 TYR cc_start: 0.8722 (p90) cc_final: 0.8169 (p90) REVERT: A 200 GLU cc_start: 0.8776 (tp30) cc_final: 0.8327 (tp30) REVERT: A 210 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8055 (mmm-85) REVERT: A 291 MET cc_start: 0.5413 (ttp) cc_final: 0.4820 (ttp) REVERT: B 136 ASP cc_start: 0.8088 (m-30) cc_final: 0.7822 (m-30) REVERT: B 169 MET cc_start: 0.7550 (ttp) cc_final: 0.7012 (ttp) REVERT: B 212 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8824 (mm-40) REVERT: B 258 TYR cc_start: 0.9172 (m-80) cc_final: 0.8120 (m-80) REVERT: B 267 MET cc_start: 0.8511 (ttp) cc_final: 0.8237 (ttm) REVERT: B 297 ASP cc_start: 0.8681 (t70) cc_final: 0.8350 (t70) REVERT: D 86 ASN cc_start: 0.9201 (t0) cc_final: 0.8979 (t0) REVERT: C 38 MET cc_start: 0.6788 (mtm) cc_final: 0.6338 (mtt) REVERT: C 76 LEU cc_start: 0.7428 (mt) cc_final: 0.7225 (mp) REVERT: C 97 HIS cc_start: 0.7874 (m170) cc_final: 0.7188 (m170) REVERT: C 141 HIS cc_start: 0.8825 (m170) cc_final: 0.8413 (m170) outliers start: 51 outliers final: 43 residues processed: 358 average time/residue: 0.1860 time to fit residues: 96.1200 Evaluate side-chains 383 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 340 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 281 ASN B 57 ASN B 233 ASN B 404 ASN D 162 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9671 Z= 0.180 Angle : 0.643 9.673 13086 Z= 0.308 Chirality : 0.043 0.259 1521 Planarity : 0.004 0.045 1683 Dihedral : 7.270 89.886 1371 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.82 % Favored : 91.09 % Rotamer: Outliers : 4.84 % Allowed : 27.44 % Favored : 67.72 % 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: -1.23 (0.24), residues: 1224 helix: 0.98 (0.23), residues: 507 sheet: -1.96 (0.56), residues: 83 loop : -2.27 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 254 HIS 0.003 0.000 HIS D 97 PHE 0.015 0.001 PHE D 68 TYR 0.011 0.001 TYR B 97 ARG 0.011 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 339 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8275 (tpp) cc_final: 0.7733 (mmp) REVERT: A 39 MET cc_start: 0.8432 (tpp) cc_final: 0.8118 (tpp) REVERT: A 82 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 118 ASP cc_start: 0.7964 (t0) cc_final: 0.6959 (t0) REVERT: A 121 GLN cc_start: 0.8494 (mp10) cc_final: 0.7992 (mp10) REVERT: A 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.7957 (tt0) REVERT: A 195 GLU cc_start: 0.8827 (pp20) cc_final: 0.8132 (pp20) REVERT: A 199 TYR cc_start: 0.8662 (p90) cc_final: 0.8166 (p90) REVERT: A 210 ARG cc_start: 0.8274 (mtp85) cc_final: 0.8012 (mmm-85) REVERT: A 264 LYS cc_start: 0.8862 (tttt) cc_final: 0.8662 (tttt) REVERT: A 275 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.7848 (m) REVERT: B 136 ASP cc_start: 0.8085 (m-30) cc_final: 0.7815 (m-30) REVERT: B 169 MET cc_start: 0.7388 (ttp) cc_final: 0.6925 (ttp) REVERT: B 212 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8830 (mm-40) REVERT: B 258 TYR cc_start: 0.9148 (m-80) cc_final: 0.8060 (m-80) REVERT: B 267 MET cc_start: 0.8524 (ttp) cc_final: 0.8268 (ttm) REVERT: B 293 MET cc_start: 0.8544 (tmm) cc_final: 0.7635 (tpt) REVERT: C 38 MET cc_start: 0.6692 (mtm) cc_final: 0.6288 (mtt) REVERT: C 97 HIS cc_start: 0.7924 (m170) cc_final: 0.7204 (m170) REVERT: C 141 HIS cc_start: 0.8804 (m170) cc_final: 0.8403 (m170) outliers start: 49 outliers final: 35 residues processed: 354 average time/residue: 0.1793 time to fit residues: 91.5462 Evaluate side-chains 368 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 332 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN D 86 ASN D 162 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9671 Z= 0.174 Angle : 0.670 10.138 13086 Z= 0.315 Chirality : 0.044 0.262 1521 Planarity : 0.004 0.049 1683 Dihedral : 7.170 88.114 1371 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.50 % Rotamer: Outliers : 4.64 % Allowed : 28.23 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1224 helix: 0.98 (0.23), residues: 511 sheet: -1.74 (0.56), residues: 86 loop : -2.31 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 254 HIS 0.002 0.000 HIS D 97 PHE 0.013 0.001 PHE A 257 TYR 0.012 0.001 TYR D 93 ARG 0.012 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 339 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8447 (tpp) cc_final: 0.8045 (tpp) REVERT: A 82 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 121 GLN cc_start: 0.8429 (mp10) cc_final: 0.8168 (mp10) REVERT: A 122 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8657 (tttt) REVERT: A 148 GLU cc_start: 0.8328 (tt0) cc_final: 0.7948 (tt0) REVERT: A 195 GLU cc_start: 0.8816 (pp20) cc_final: 0.8157 (pp20) REVERT: A 199 TYR cc_start: 0.8656 (p90) cc_final: 0.8059 (p90) REVERT: A 200 GLU cc_start: 0.8712 (tp30) cc_final: 0.8351 (tp30) REVERT: A 210 ARG cc_start: 0.8256 (mtp85) cc_final: 0.8015 (mmm-85) REVERT: A 317 GLN cc_start: 0.8887 (tp40) cc_final: 0.8447 (tp40) REVERT: B 136 ASP cc_start: 0.8077 (m-30) cc_final: 0.7804 (m-30) REVERT: B 169 MET cc_start: 0.7382 (ttp) cc_final: 0.6974 (ttp) REVERT: B 267 MET cc_start: 0.8494 (ttp) cc_final: 0.8245 (ttm) REVERT: B 293 MET cc_start: 0.8520 (tmm) cc_final: 0.7637 (tpt) REVERT: D 37 MET cc_start: 0.5200 (tmm) cc_final: 0.4368 (tmm) REVERT: D 38 MET cc_start: 0.4045 (mtm) cc_final: 0.3277 (mpp) REVERT: C 38 MET cc_start: 0.6860 (mtm) cc_final: 0.6402 (mtt) REVERT: C 97 HIS cc_start: 0.7897 (m170) cc_final: 0.7187 (m170) REVERT: C 141 HIS cc_start: 0.8801 (m170) cc_final: 0.8398 (m90) REVERT: C 150 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8554 (tp30) outliers start: 47 outliers final: 39 residues processed: 352 average time/residue: 0.1762 time to fit residues: 89.9977 Evaluate side-chains 365 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 325 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN B 57 ASN B 212 GLN D 123 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9671 Z= 0.166 Angle : 0.660 10.259 13086 Z= 0.312 Chirality : 0.044 0.266 1521 Planarity : 0.004 0.050 1683 Dihedral : 6.800 85.367 1371 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer: Outliers : 4.34 % Allowed : 28.63 % Favored : 67.03 % 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: -1.15 (0.25), residues: 1224 helix: 0.97 (0.23), residues: 513 sheet: -1.77 (0.58), residues: 83 loop : -2.21 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 254 HIS 0.002 0.000 HIS D 97 PHE 0.012 0.001 PHE A 257 TYR 0.014 0.001 TYR D 93 ARG 0.013 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 336 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8087 (tpp) cc_final: 0.7641 (mmp) REVERT: A 52 GLU cc_start: 0.8816 (tt0) cc_final: 0.8612 (tt0) REVERT: A 82 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 121 GLN cc_start: 0.8404 (mp10) cc_final: 0.8148 (mp10) REVERT: A 148 GLU cc_start: 0.8295 (tt0) cc_final: 0.7912 (tt0) REVERT: A 195 GLU cc_start: 0.8854 (pp20) cc_final: 0.8177 (pp20) REVERT: A 199 TYR cc_start: 0.8613 (p90) cc_final: 0.8018 (p90) REVERT: A 200 GLU cc_start: 0.8649 (tp30) cc_final: 0.8250 (tp30) REVERT: A 210 ARG cc_start: 0.8216 (mtp85) cc_final: 0.8011 (mmm-85) REVERT: B 48 MET cc_start: 0.8878 (mmp) cc_final: 0.8520 (mmp) REVERT: B 136 ASP cc_start: 0.8099 (m-30) cc_final: 0.7812 (m-30) REVERT: B 169 MET cc_start: 0.7231 (ttp) cc_final: 0.6888 (ttp) REVERT: B 267 MET cc_start: 0.8397 (ttp) cc_final: 0.8137 (ttm) REVERT: B 293 MET cc_start: 0.8475 (tmm) cc_final: 0.7646 (tpt) REVERT: D 37 MET cc_start: 0.5297 (tmm) cc_final: 0.4476 (tmm) REVERT: D 38 MET cc_start: 0.4104 (mtm) cc_final: 0.3278 (mpp) REVERT: C 38 MET cc_start: 0.6835 (mtm) cc_final: 0.6400 (mtt) REVERT: C 83 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: C 97 HIS cc_start: 0.7979 (m170) cc_final: 0.7209 (m170) REVERT: C 141 HIS cc_start: 0.8775 (m170) cc_final: 0.8400 (m90) REVERT: C 150 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8523 (tp30) outliers start: 44 outliers final: 36 residues processed: 351 average time/residue: 0.1700 time to fit residues: 86.7885 Evaluate side-chains 375 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 337 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 58 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 102 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 233 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9671 Z= 0.275 Angle : 0.717 10.867 13086 Z= 0.348 Chirality : 0.046 0.248 1521 Planarity : 0.004 0.051 1683 Dihedral : 7.071 82.771 1371 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.21 % Favored : 89.71 % Rotamer: Outliers : 4.84 % Allowed : 29.02 % Favored : 66.14 % 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: -1.34 (0.24), residues: 1224 helix: 0.84 (0.23), residues: 510 sheet: -1.81 (0.57), residues: 86 loop : -2.33 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.003 0.001 HIS D 97 PHE 0.018 0.002 PHE A 257 TYR 0.012 0.001 TYR D 93 ARG 0.013 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 341 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8262 (tpp) cc_final: 0.7669 (mmp) REVERT: A 82 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8244 (tm-30) REVERT: A 118 ASP cc_start: 0.7986 (t0) cc_final: 0.6943 (t0) REVERT: A 121 GLN cc_start: 0.8451 (mp10) cc_final: 0.7880 (mp10) REVERT: A 148 GLU cc_start: 0.8404 (tt0) cc_final: 0.8047 (tt0) REVERT: A 195 GLU cc_start: 0.8844 (pp20) cc_final: 0.8080 (pp20) REVERT: A 199 TYR cc_start: 0.8738 (p90) cc_final: 0.8114 (p90) REVERT: A 200 GLU cc_start: 0.8791 (tp30) cc_final: 0.8394 (tp30) REVERT: A 245 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7943 (mptt) REVERT: A 292 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 136 ASP cc_start: 0.8139 (m-30) cc_final: 0.7877 (m-30) REVERT: B 146 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: B 169 MET cc_start: 0.7398 (ttp) cc_final: 0.6974 (ttp) REVERT: B 212 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8671 (mm110) REVERT: B 267 MET cc_start: 0.8501 (ttp) cc_final: 0.8206 (ttm) REVERT: B 293 MET cc_start: 0.8586 (tmm) cc_final: 0.7642 (tpt) REVERT: D 37 MET cc_start: 0.5219 (tmm) cc_final: 0.4623 (tmm) REVERT: C 38 MET cc_start: 0.6939 (mtm) cc_final: 0.6507 (mtt) REVERT: C 83 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: C 97 HIS cc_start: 0.8154 (m170) cc_final: 0.7371 (m170) REVERT: C 141 HIS cc_start: 0.8803 (m170) cc_final: 0.8505 (m170) REVERT: C 150 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (tp30) outliers start: 49 outliers final: 41 residues processed: 356 average time/residue: 0.1882 time to fit residues: 95.2265 Evaluate side-chains 382 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 337 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 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 57 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.197652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149866 restraints weight = 13255.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155565 restraints weight = 6467.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159297 restraints weight = 3986.560| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9671 Z= 0.189 Angle : 0.679 10.670 13086 Z= 0.324 Chirality : 0.045 0.264 1521 Planarity : 0.004 0.055 1683 Dihedral : 6.725 79.071 1371 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.48 % Favored : 90.44 % Rotamer: Outliers : 4.05 % Allowed : 30.70 % Favored : 65.25 % 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: -1.29 (0.24), residues: 1224 helix: 0.89 (0.23), residues: 514 sheet: -1.84 (0.56), residues: 88 loop : -2.33 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 254 HIS 0.002 0.000 HIS D 97 PHE 0.014 0.001 PHE A 257 TYR 0.014 0.001 TYR D 93 ARG 0.013 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.34 seconds wall clock time: 44 minutes 20.89 seconds (2660.89 seconds total)