Starting phenix.real_space_refine on Tue Sep 24 21:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/09_2024/8ija_35483_neut.cif" } resolution = 2.69 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= 0.024 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 67 5.16 5 C 5653 2.51 5 N 1506 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8845 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2357 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1699 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.66 Number of scatterers: 8845 At special positions: 0 Unit cell: (87.15, 119.52, 130.31, 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 67 16.00 O 1619 8.00 N 1506 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 16 sheets defined 36.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 23 through 55 removed outlier: 3.740A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.610A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.646A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.836A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 131 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.705A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 188 through 218 removed outlier: 3.762A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 262 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.689A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.606A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.715A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.233A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.507A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.705A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA3, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.301A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.552A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.687A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.138A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.758A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1260 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: 2.72 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2656 1.34 - 1.46: 2304 1.46 - 1.59: 3981 1.59 - 1.71: 0 1.71 - 1.84: 97 Bond restraints: 9038 Sorted by residual: bond pdb=" ND1 HIS A 9 " pdb=" CE1 HIS A 9 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.83e+01 bond pdb=" ND1 HIS A 259 " pdb=" CE1 HIS A 259 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" CG ASN A 17 " pdb=" OD1 ASN A 17 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.65e+01 bond pdb=" ND1 HIS A 133 " pdb=" CE1 HIS A 133 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.64e+01 bond pdb=" CD2 HIS A 133 " pdb=" NE2 HIS A 133 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.37e+01 ... (remaining 9033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 12206 6.90 - 13.80: 22 13.80 - 20.71: 7 20.71 - 27.61: 5 27.61 - 34.51: 2 Bond angle restraints: 12242 Sorted by residual: angle pdb=" N TYR A 295 " pdb=" CA TYR A 295 " pdb=" C TYR A 295 " ideal model delta sigma weight residual 111.69 146.20 -34.51 1.23e+00 6.61e-01 7.87e+02 angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 111.24 142.05 -30.81 1.29e+00 6.01e-01 5.70e+02 angle pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" C CYS C 325 " ideal model delta sigma weight residual 112.86 134.01 -21.15 1.22e+00 6.72e-01 3.01e+02 angle pdb=" C VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta sigma weight residual 111.81 91.92 19.89 1.37e+00 5.33e-01 2.11e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta sigma weight residual 110.33 89.57 20.76 1.50e+00 4.44e-01 1.91e+02 ... (remaining 12237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4517 17.82 - 35.64: 590 35.64 - 53.47: 179 53.47 - 71.29: 33 71.29 - 89.11: 18 Dihedral angle restraints: 5337 sinusoidal: 2050 harmonic: 3287 Sorted by residual: dihedral pdb=" C VAL C 201 " pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta harmonic sigma weight residual -122.00 -90.73 -31.27 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta harmonic sigma weight residual 122.80 95.32 27.48 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C CYS C 325 " pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" CB CYS C 325 " ideal model delta harmonic sigma weight residual -122.60 -143.50 20.90 0 2.50e+00 1.60e-01 6.99e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 1375 0.260 - 0.519: 5 0.519 - 0.778: 2 0.778 - 1.038: 0 1.038 - 1.297: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR A 295 " pdb=" N TYR A 295 " pdb=" C TYR A 295 " pdb=" CB TYR A 295 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA ARG A 270 " pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CB ARG A 270 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" CA CYS C 325 " pdb=" N CYS C 325 " pdb=" C CYS C 325 " pdb=" CB CYS C 325 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.94e+01 ... (remaining 1383 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.111 2.00e-02 2.50e+03 6.51e-02 8.49e+01 pdb=" CG TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 91 " -0.099 2.00e-02 2.50e+03 5.25e-02 6.89e+01 pdb=" CG TRP A 91 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 91 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP A 91 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 91 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 91 " 0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 91 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 91 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP A 91 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 87 " 0.062 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR A 87 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 87 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 87 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 87 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 87 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 87 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 87 " 0.035 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 51 2.41 - 3.04: 5361 3.04 - 3.66: 13377 3.66 - 4.28: 21213 4.28 - 4.90: 35863 Nonbonded interactions: 75865 Sorted by model distance: nonbonded pdb=" O THR C 324 " pdb=" CG2 THR C 327 " model vdw 1.793 3.460 nonbonded pdb=" O ARG A 270 " pdb=" NH1 ARG A 270 " model vdw 1.900 3.120 nonbonded pdb=" O VAL C 201 " pdb=" CG2 VAL C 201 " model vdw 1.912 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.046 3.040 nonbonded pdb=" OG SER A 298 " pdb=" O GLY C 352 " model vdw 2.049 3.040 ... (remaining 75860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 9038 Z= 0.303 Angle : 1.105 34.511 12242 Z= 0.714 Chirality : 0.084 1.297 1386 Planarity : 0.005 0.065 1548 Dihedral : 18.233 89.108 3198 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 5.37 % Allowed : 27.37 % Favored : 67.26 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1118 helix: 1.55 (0.27), residues: 376 sheet: -0.03 (0.30), residues: 281 loop : -1.06 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.003 TRP A 91 HIS 0.010 0.001 HIS A 189 PHE 0.023 0.002 PHE A 276 TYR 0.111 0.003 TYR A 284 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 1.378 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 38 PHE cc_start: 0.6715 (t80) cc_final: 0.6493 (t80) REVERT: A 79 CYS cc_start: 0.7974 (m) cc_final: 0.7618 (m) REVERT: A 156 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7274 (mm) REVERT: A 258 LEU cc_start: 0.7171 (pp) cc_final: 0.6332 (mt) REVERT: C 309 ASP cc_start: 0.8273 (m-30) cc_final: 0.7952 (m-30) REVERT: B 46 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7630 (mpt180) outliers start: 51 outliers final: 43 residues processed: 185 average time/residue: 1.2664 time to fit residues: 250.1979 Evaluate side-chains 172 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.0030 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 86 ASN C 188 HIS G 59 ASN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9038 Z= 0.168 Angle : 0.557 6.521 12242 Z= 0.294 Chirality : 0.042 0.183 1386 Planarity : 0.004 0.045 1548 Dihedral : 7.777 59.317 1291 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.47 % Allowed : 25.47 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1118 helix: 1.81 (0.27), residues: 385 sheet: 0.08 (0.30), residues: 286 loop : -1.09 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.001 HIS A 259 PHE 0.020 0.001 PHE A 38 TYR 0.017 0.001 TYR S 178 ARG 0.006 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 140 time to evaluate : 1.033 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 79 CYS cc_start: 0.7858 (m) cc_final: 0.7624 (m) REVERT: A 80 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6714 (mm) REVERT: A 106 MET cc_start: 0.7291 (mmm) cc_final: 0.7041 (mmm) REVERT: A 110 ASN cc_start: 0.7645 (m-40) cc_final: 0.6730 (m-40) REVERT: A 150 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7967 (tt) REVERT: C 209 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8475 (pttm) REVERT: B 46 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7650 (mpt180) REVERT: B 268 ASN cc_start: 0.7973 (t0) cc_final: 0.7580 (t0) outliers start: 52 outliers final: 20 residues processed: 177 average time/residue: 1.2678 time to fit residues: 238.5901 Evaluate side-chains 149 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS C 188 HIS B 75 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9038 Z= 0.297 Angle : 0.590 6.713 12242 Z= 0.307 Chirality : 0.044 0.172 1386 Planarity : 0.004 0.046 1548 Dihedral : 6.391 56.584 1241 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.89 % Allowed : 25.16 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1118 helix: 1.80 (0.27), residues: 386 sheet: 0.11 (0.30), residues: 287 loop : -1.14 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.002 PHE C 189 TYR 0.014 0.002 TYR S 178 ARG 0.004 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 131 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7433 (tttt) cc_final: 0.7021 (mtpm) REVERT: A 79 CYS cc_start: 0.7948 (m) cc_final: 0.7622 (m) REVERT: A 80 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6758 (mm) REVERT: A 106 MET cc_start: 0.7399 (mmm) cc_final: 0.7054 (tpp) REVERT: A 110 ASN cc_start: 0.7680 (m-40) cc_final: 0.6796 (m-40) REVERT: A 112 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: A 227 LYS cc_start: 0.6457 (mmmm) cc_final: 0.6233 (mmmm) REVERT: A 257 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6548 (mp) REVERT: C 209 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8546 (pttm) REVERT: B 268 ASN cc_start: 0.7970 (t0) cc_final: 0.7571 (t0) REVERT: S 135 VAL cc_start: 0.7581 (m) cc_final: 0.7310 (p) outliers start: 56 outliers final: 25 residues processed: 168 average time/residue: 1.2735 time to fit residues: 227.4878 Evaluate side-chains 160 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 9038 Z= 0.438 Angle : 0.645 7.662 12242 Z= 0.337 Chirality : 0.047 0.206 1386 Planarity : 0.004 0.045 1548 Dihedral : 6.375 57.715 1237 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.89 % Allowed : 25.05 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1118 helix: 1.68 (0.27), residues: 383 sheet: 0.03 (0.31), residues: 287 loop : -1.24 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.002 PHE A 38 TYR 0.018 0.002 TYR A 269 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 134 time to evaluate : 1.115 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7449 (tttt) cc_final: 0.7073 (mtpm) REVERT: A 80 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6920 (mm) REVERT: A 97 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5273 (OUTLIER) REVERT: A 110 ASN cc_start: 0.7702 (m-40) cc_final: 0.7034 (m-40) REVERT: A 257 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6556 (mp) REVERT: C 209 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8508 (pttm) REVERT: C 309 ASP cc_start: 0.8290 (m-30) cc_final: 0.7739 (m-30) REVERT: S 135 VAL cc_start: 0.7575 (m) cc_final: 0.7309 (p) outliers start: 56 outliers final: 28 residues processed: 171 average time/residue: 1.2626 time to fit residues: 229.8423 Evaluate side-chains 168 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.0270 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9038 Z= 0.221 Angle : 0.566 8.094 12242 Z= 0.294 Chirality : 0.042 0.165 1386 Planarity : 0.004 0.041 1548 Dihedral : 5.983 54.746 1237 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.68 % Allowed : 26.32 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1118 helix: 1.79 (0.27), residues: 384 sheet: 0.04 (0.31), residues: 287 loop : -1.13 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.016 0.001 TYR S 178 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 1.058 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7411 (tttt) cc_final: 0.7093 (mtpm) REVERT: A 80 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6697 (mm) REVERT: A 112 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: A 166 LYS cc_start: 0.5632 (tppt) cc_final: 0.5346 (mmtm) REVERT: A 257 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6518 (mp) REVERT: C 209 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8451 (pttm) REVERT: C 309 ASP cc_start: 0.8315 (m-30) cc_final: 0.8010 (m-30) REVERT: B 268 ASN cc_start: 0.7961 (t0) cc_final: 0.7538 (t0) REVERT: G 21 MET cc_start: 0.7532 (tpp) cc_final: 0.7264 (tpp) REVERT: S 135 VAL cc_start: 0.7478 (m) cc_final: 0.7201 (p) outliers start: 54 outliers final: 21 residues processed: 172 average time/residue: 1.2398 time to fit residues: 226.9299 Evaluate side-chains 155 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9038 Z= 0.231 Angle : 0.570 8.663 12242 Z= 0.295 Chirality : 0.043 0.162 1386 Planarity : 0.004 0.041 1548 Dihedral : 5.725 55.865 1234 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.47 % Allowed : 26.95 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1118 helix: 1.82 (0.27), residues: 384 sheet: 0.05 (0.31), residues: 285 loop : -1.10 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.021 0.001 PHE A 38 TYR 0.021 0.001 TYR A 269 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 1.059 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7404 (tttt) cc_final: 0.7109 (mtpm) REVERT: A 34 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4856 (mp) REVERT: A 80 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6843 (mm) REVERT: A 94 LYS cc_start: 0.7197 (pptt) cc_final: 0.6134 (mmmt) REVERT: A 112 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: A 166 LYS cc_start: 0.5533 (tppt) cc_final: 0.5146 (mmtm) REVERT: A 257 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6504 (mp) REVERT: C 209 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8436 (pttm) REVERT: C 309 ASP cc_start: 0.8306 (m-30) cc_final: 0.8003 (m-30) REVERT: B 17 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: B 268 ASN cc_start: 0.7993 (t0) cc_final: 0.7585 (t0) REVERT: G 21 MET cc_start: 0.7523 (tpp) cc_final: 0.7275 (tpp) REVERT: S 135 VAL cc_start: 0.7464 (m) cc_final: 0.7189 (p) outliers start: 52 outliers final: 21 residues processed: 172 average time/residue: 1.3146 time to fit residues: 240.7851 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9038 Z= 0.176 Angle : 0.562 9.289 12242 Z= 0.288 Chirality : 0.042 0.173 1386 Planarity : 0.004 0.039 1548 Dihedral : 5.294 56.756 1233 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.11 % Allowed : 28.11 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1118 helix: 1.91 (0.27), residues: 384 sheet: 0.03 (0.31), residues: 286 loop : -1.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.023 0.001 TYR A 269 ARG 0.007 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 0.974 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7429 (tttt) cc_final: 0.7060 (mtpm) REVERT: A 34 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4533 (mp) REVERT: A 80 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6771 (mm) REVERT: A 94 LYS cc_start: 0.7119 (pptt) cc_final: 0.6056 (mmmt) REVERT: A 112 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: A 257 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6488 (mp) REVERT: A 258 LEU cc_start: 0.6972 (pp) cc_final: 0.6130 (mm) REVERT: C 209 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8452 (pttm) REVERT: C 309 ASP cc_start: 0.8288 (m-30) cc_final: 0.8019 (m-30) REVERT: B 268 ASN cc_start: 0.7998 (t0) cc_final: 0.7588 (t0) REVERT: G 21 MET cc_start: 0.7513 (tpp) cc_final: 0.7271 (tpp) REVERT: S 135 VAL cc_start: 0.7375 (m) cc_final: 0.7104 (p) outliers start: 39 outliers final: 21 residues processed: 167 average time/residue: 1.2327 time to fit residues: 219.0336 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9038 Z= 0.230 Angle : 0.579 8.988 12242 Z= 0.296 Chirality : 0.043 0.171 1386 Planarity : 0.004 0.039 1548 Dihedral : 5.002 45.984 1229 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.32 % Allowed : 27.79 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1118 helix: 1.91 (0.27), residues: 384 sheet: 0.05 (0.31), residues: 285 loop : -1.06 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.020 0.001 TYR A 269 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.188 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7423 (tttt) cc_final: 0.7072 (mtpm) REVERT: A 34 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4529 (mp) REVERT: A 80 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6735 (mm) REVERT: A 94 LYS cc_start: 0.7149 (pptt) cc_final: 0.6146 (mmmt) REVERT: A 97 ASP cc_start: 0.5486 (OUTLIER) cc_final: 0.5224 (OUTLIER) REVERT: A 112 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 257 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6494 (mp) REVERT: A 258 LEU cc_start: 0.6956 (pp) cc_final: 0.6093 (mm) REVERT: C 209 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8414 (pttm) REVERT: B 17 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: B 268 ASN cc_start: 0.8005 (t0) cc_final: 0.7591 (t0) REVERT: G 21 MET cc_start: 0.7518 (tpp) cc_final: 0.7288 (tpp) REVERT: S 135 VAL cc_start: 0.7370 (m) cc_final: 0.7105 (p) outliers start: 41 outliers final: 25 residues processed: 162 average time/residue: 1.2349 time to fit residues: 213.0933 Evaluate side-chains 157 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9038 Z= 0.225 Angle : 0.596 10.877 12242 Z= 0.302 Chirality : 0.043 0.221 1386 Planarity : 0.004 0.057 1548 Dihedral : 4.976 42.137 1229 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.58 % Allowed : 28.84 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1118 helix: 1.98 (0.27), residues: 379 sheet: 0.05 (0.31), residues: 285 loop : -1.02 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.020 0.001 TYR A 269 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.082 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7406 (tttt) cc_final: 0.7085 (mtpm) REVERT: A 34 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4532 (mp) REVERT: A 80 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6881 (mm) REVERT: A 94 LYS cc_start: 0.7121 (pptt) cc_final: 0.6126 (mmmt) REVERT: A 112 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: A 257 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6516 (mp) REVERT: A 258 LEU cc_start: 0.6889 (pp) cc_final: 0.6099 (mm) REVERT: C 209 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8381 (pttm) REVERT: B 268 ASN cc_start: 0.7988 (t0) cc_final: 0.7575 (t0) REVERT: S 135 VAL cc_start: 0.7358 (m) cc_final: 0.7095 (p) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 1.2137 time to fit residues: 198.0816 Evaluate side-chains 153 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9038 Z= 0.197 Angle : 0.604 10.614 12242 Z= 0.303 Chirality : 0.042 0.192 1386 Planarity : 0.004 0.039 1548 Dihedral : 4.828 40.437 1229 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.05 % Allowed : 29.58 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1118 helix: 1.98 (0.27), residues: 381 sheet: 0.06 (0.31), residues: 286 loop : -0.99 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.020 0.001 TYR A 269 ARG 0.008 0.000 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.193 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7363 (tttt) cc_final: 0.7099 (mtpm) REVERT: A 34 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4465 (mp) REVERT: A 80 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6900 (mm) REVERT: A 94 LYS cc_start: 0.6958 (pptt) cc_final: 0.6003 (mmmt) REVERT: A 112 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 257 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6500 (mp) REVERT: A 258 LEU cc_start: 0.6849 (pp) cc_final: 0.6057 (mm) REVERT: C 209 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8384 (pttm) REVERT: B 268 ASN cc_start: 0.7965 (t0) cc_final: 0.7551 (t0) REVERT: S 135 VAL cc_start: 0.7327 (m) cc_final: 0.7067 (p) outliers start: 29 outliers final: 22 residues processed: 152 average time/residue: 1.2766 time to fit residues: 206.6514 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100504 restraints weight = 10427.569| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.33 r_work: 0.3000 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9038 Z= 0.311 Angle : 0.652 11.176 12242 Z= 0.328 Chirality : 0.044 0.192 1386 Planarity : 0.004 0.040 1548 Dihedral : 4.940 41.499 1228 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.16 % Allowed : 29.89 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1118 helix: 1.92 (0.27), residues: 379 sheet: 0.02 (0.31), residues: 287 loop : -1.05 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS C 322 PHE 0.019 0.002 PHE A 38 TYR 0.019 0.002 TYR A 269 ARG 0.008 0.001 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4326.35 seconds wall clock time: 76 minutes 21.84 seconds (4581.84 seconds total)