Starting phenix.real_space_refine on Fri Jul 19 19:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/07_2024/8uh3_42245.cif" } resolution = 3.31 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= -0.001 sd= 0.078 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 63 5.16 5 C 5631 2.51 5 N 1457 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8759 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2168 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 132 Unusual residues: {'CLR': 4, 'WOQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.66 Number of scatterers: 8759 At special positions: 0 Unit cell: (91.46, 117.284, 123.74, 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 63 16.00 O 1608 8.00 N 1457 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.378A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.983A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.828A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.068A pdb=" N CYS A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.742A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 Processing helix chain 'D' and resid 20 through 50 Processing helix chain 'D' and resid 55 through 75 Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.509A pdb=" N VAL D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 126 removed outlier: 3.623A pdb=" N MET D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.968A pdb=" N ARG D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.730A pdb=" N PHE D 159 " --> pdb=" O MET D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 191 through 210 removed outlier: 3.785A pdb=" N LYS D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 286 through 316 removed outlier: 3.610A pdb=" N TRP D 304 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 322 through 346 removed outlier: 3.788A pdb=" N GLY D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Proline residue: D 341 - end of helix Processing helix chain 'D' and resid 348 through 359 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.049A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.716A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.231A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.602A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.648A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.634A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.709A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.804A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.246A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.664A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.704A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.589A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1290 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: 2.96 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2747 1.34 - 1.46: 2120 1.46 - 1.58: 3993 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 8951 Sorted by residual: bond pdb=" CA ALA B 11 " pdb=" C ALA B 11 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.11e+00 bond pdb=" CA ALA B 11 " pdb=" CB ALA B 11 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.55e-02 4.16e+03 4.18e+00 bond pdb=" C ALA B 11 " pdb=" N GLU B 12 " ideal model delta sigma weight residual 1.335 1.311 0.024 1.30e-02 5.92e+03 3.45e+00 bond pdb=" C ALA B 11 " pdb=" O ALA B 11 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.15e-02 7.56e+03 2.19e+00 bond pdb=" C3 WOQ D 405 " pdb=" C4 WOQ D 405 " ideal model delta sigma weight residual 1.347 1.321 0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 8946 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.80: 118 104.80 - 112.11: 4597 112.11 - 119.43: 2941 119.43 - 126.75: 4365 126.75 - 134.06: 124 Bond angle restraints: 12145 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.56 109.80 4.76 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N ALA B 11 " pdb=" CA ALA B 11 " pdb=" C ALA B 11 " ideal model delta sigma weight residual 111.07 107.90 3.17 1.07e+00 8.73e-01 8.78e+00 angle pdb=" N PRO D 156 " pdb=" CA PRO D 156 " pdb=" C PRO D 156 " ideal model delta sigma weight residual 110.70 114.26 -3.56 1.22e+00 6.72e-01 8.51e+00 angle pdb=" CA ARG B 197 " pdb=" C ARG B 197 " pdb=" N LEU B 198 " ideal model delta sigma weight residual 119.26 116.34 2.92 1.14e+00 7.69e-01 6.57e+00 angle pdb=" CB MET A 247 " pdb=" CG MET A 247 " pdb=" SD MET A 247 " ideal model delta sigma weight residual 112.70 120.28 -7.58 3.00e+00 1.11e-01 6.39e+00 ... (remaining 12140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 5207 23.79 - 47.58: 269 47.58 - 71.38: 21 71.38 - 95.17: 12 95.17 - 118.96: 4 Dihedral angle restraints: 5513 sinusoidal: 2323 harmonic: 3190 Sorted by residual: dihedral pdb=" C10 CLR D 402 " pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " ideal model delta sinusoidal sigma weight residual -56.83 62.13 -118.96 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " pdb=" O1 CLR D 402 " ideal model delta sinusoidal sigma weight residual 180.04 70.31 109.73 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " pdb=" C4 CLR D 402 " ideal model delta sinusoidal sigma weight residual 57.41 -50.54 107.95 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 5510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 997 0.041 - 0.081: 302 0.081 - 0.122: 86 0.122 - 0.162: 9 0.162 - 0.203: 2 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CB THR D 148 " pdb=" CA THR D 148 " pdb=" OG1 THR D 148 " pdb=" CG2 THR D 148 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1393 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 156 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO D 157 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C12 WOQ D 405 " 0.025 2.00e-02 2.50e+03 1.40e-02 3.91e+00 pdb=" C13 WOQ D 405 " -0.012 2.00e-02 2.50e+03 pdb=" C14 WOQ D 405 " -0.017 2.00e-02 2.50e+03 pdb=" C15 WOQ D 405 " -0.003 2.00e-02 2.50e+03 pdb=" C16 WOQ D 405 " 0.014 2.00e-02 2.50e+03 pdb=" C17 WOQ D 405 " 0.010 2.00e-02 2.50e+03 pdb=" C18 WOQ D 405 " -0.005 2.00e-02 2.50e+03 pdb=" C3 WOQ D 405 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 201 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" CG ASP E 201 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP E 201 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP E 201 " 0.009 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 625 2.74 - 3.28: 8857 3.28 - 3.82: 14771 3.82 - 4.36: 17754 4.36 - 4.90: 30945 Nonbonded interactions: 72952 Sorted by model distance: nonbonded pdb=" O PHE A 354 " pdb=" OH TYR D 213 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP D 119 " pdb=" OH TYR D 130 " model vdw 2.199 2.440 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.213 2.520 nonbonded pdb=" NH1 ARG E 202 " pdb=" OE1 GLU E 220 " model vdw 2.218 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.244 2.440 ... (remaining 72947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.003 0.032 8951 Z= 0.209 Angle : 0.570 7.585 12145 Z= 0.307 Chirality : 0.042 0.203 1396 Planarity : 0.004 0.074 1488 Dihedral : 14.491 118.960 3443 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1078 helix: 1.25 (0.27), residues: 392 sheet: -0.40 (0.32), residues: 248 loop : -0.03 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE D 307 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: B 145 TYR cc_start: 0.9099 (p90) cc_final: 0.8605 (p90) REVERT: B 189 SER cc_start: 0.8543 (p) cc_final: 0.8311 (p) REVERT: B 291 ASP cc_start: 0.7488 (t70) cc_final: 0.7276 (t0) REVERT: A 24 ARG cc_start: 0.6786 (ttp-110) cc_final: 0.6572 (ttp-170) REVERT: G 20 LYS cc_start: 0.8423 (ptpp) cc_final: 0.7755 (mtmm) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.2677 time to fit residues: 69.3915 Evaluate side-chains 171 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8951 Z= 0.327 Angle : 0.578 7.081 12145 Z= 0.300 Chirality : 0.043 0.154 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.396 94.329 1472 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.12 % Allowed : 11.02 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.40 (0.26), residues: 1078 helix: 1.32 (0.26), residues: 387 sheet: -0.60 (0.31), residues: 265 loop : 0.05 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS E 167 PHE 0.014 0.002 PHE E 29 TYR 0.017 0.002 TYR E 190 ARG 0.004 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.064 Fit side-chains REVERT: B 163 ASP cc_start: 0.7987 (t0) cc_final: 0.7771 (t0) REVERT: B 189 SER cc_start: 0.8633 (p) cc_final: 0.8385 (p) REVERT: B 291 ASP cc_start: 0.7585 (t70) cc_final: 0.7183 (t0) REVERT: D 27 MET cc_start: 0.6989 (ptp) cc_final: 0.6699 (ttt) outliers start: 20 outliers final: 17 residues processed: 191 average time/residue: 0.2734 time to fit residues: 67.3858 Evaluate side-chains 188 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN A 256 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8951 Z= 0.226 Angle : 0.529 6.823 12145 Z= 0.278 Chirality : 0.041 0.139 1396 Planarity : 0.004 0.077 1488 Dihedral : 8.320 95.594 1472 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 13.56 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.43 (0.26), residues: 1078 helix: 1.36 (0.26), residues: 387 sheet: -0.52 (0.31), residues: 264 loop : -0.01 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE D 347 TYR 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.028 Fit side-chains REVERT: B 59 TYR cc_start: 0.8461 (m-80) cc_final: 0.8248 (m-80) REVERT: B 163 ASP cc_start: 0.7869 (t0) cc_final: 0.7634 (t0) REVERT: B 189 SER cc_start: 0.8623 (p) cc_final: 0.8364 (p) REVERT: B 291 ASP cc_start: 0.7568 (t70) cc_final: 0.7171 (t0) REVERT: A 337 ASP cc_start: 0.8337 (m-30) cc_final: 0.8052 (m-30) REVERT: D 23 MET cc_start: 0.7858 (mtt) cc_final: 0.7331 (mmp) REVERT: D 27 MET cc_start: 0.7055 (ptp) cc_final: 0.6772 (ttt) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.2645 time to fit residues: 64.2148 Evaluate side-chains 188 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8951 Z= 0.168 Angle : 0.509 6.469 12145 Z= 0.266 Chirality : 0.041 0.149 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.254 97.203 1472 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.44 % Allowed : 15.47 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.62 (0.26), residues: 1078 helix: 1.49 (0.27), residues: 388 sheet: -0.35 (0.32), residues: 254 loop : 0.06 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS E 167 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8416 (m-80) cc_final: 0.8164 (m-80) REVERT: B 163 ASP cc_start: 0.7938 (t0) cc_final: 0.7632 (t0) REVERT: B 291 ASP cc_start: 0.7582 (t70) cc_final: 0.7114 (t0) REVERT: D 23 MET cc_start: 0.7892 (mtt) cc_final: 0.7376 (mmp) REVERT: D 27 MET cc_start: 0.6987 (ptp) cc_final: 0.6759 (ttt) REVERT: D 130 TYR cc_start: 0.7777 (t80) cc_final: 0.7520 (t80) outliers start: 23 outliers final: 19 residues processed: 190 average time/residue: 0.2649 time to fit residues: 65.3384 Evaluate side-chains 190 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 0.0040 chunk 26 optimal weight: 3.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 333 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8951 Z= 0.271 Angle : 0.544 7.772 12145 Z= 0.283 Chirality : 0.042 0.138 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.341 97.872 1472 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.44 % Allowed : 16.63 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.50 (0.26), residues: 1078 helix: 1.41 (0.27), residues: 387 sheet: -0.50 (0.32), residues: 257 loop : 0.03 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 88 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE D 347 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 0.942 Fit side-chains REVERT: B 59 TYR cc_start: 0.8457 (m-80) cc_final: 0.8225 (m-80) REVERT: B 163 ASP cc_start: 0.7913 (t0) cc_final: 0.7413 (t0) REVERT: B 291 ASP cc_start: 0.7605 (t70) cc_final: 0.7145 (t0) REVERT: D 23 MET cc_start: 0.7859 (mtt) cc_final: 0.7378 (mmp) REVERT: D 27 MET cc_start: 0.6998 (ptp) cc_final: 0.6713 (ttp) REVERT: D 74 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (tt) outliers start: 23 outliers final: 18 residues processed: 191 average time/residue: 0.2573 time to fit residues: 63.9778 Evaluate side-chains 188 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8951 Z= 0.192 Angle : 0.522 6.655 12145 Z= 0.272 Chirality : 0.041 0.153 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.252 97.958 1472 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 16.84 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.56 (0.26), residues: 1078 helix: 1.44 (0.27), residues: 394 sheet: -0.34 (0.32), residues: 253 loop : -0.04 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7910 (t0) cc_final: 0.7445 (t0) REVERT: B 214 ARG cc_start: 0.7669 (mmp-170) cc_final: 0.7466 (mmp-170) REVERT: B 291 ASP cc_start: 0.7645 (t70) cc_final: 0.7163 (t0) REVERT: D 23 MET cc_start: 0.7733 (mtt) cc_final: 0.7319 (mmp) REVERT: D 27 MET cc_start: 0.6906 (ptp) cc_final: 0.6679 (ttp) REVERT: D 74 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7304 (tt) outliers start: 29 outliers final: 23 residues processed: 195 average time/residue: 0.2623 time to fit residues: 66.8336 Evaluate side-chains 196 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 64 optimal weight: 0.0000 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 overall best weight: 0.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8951 Z= 0.130 Angle : 0.512 8.809 12145 Z= 0.265 Chirality : 0.040 0.154 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.151 97.960 1472 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.91 % Allowed : 19.17 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.62 (0.26), residues: 1078 helix: 1.49 (0.27), residues: 394 sheet: -0.21 (0.33), residues: 253 loop : -0.07 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 88 HIS 0.002 0.000 HIS B 54 PHE 0.014 0.001 PHE D 347 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7843 (t0) cc_final: 0.7297 (t0) REVERT: B 291 ASP cc_start: 0.7591 (t70) cc_final: 0.7107 (t0) REVERT: A 53 MET cc_start: 0.6215 (mpp) cc_final: 0.5739 (mtm) REVERT: D 23 MET cc_start: 0.7689 (mtt) cc_final: 0.7300 (mmp) REVERT: D 74 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7201 (tt) outliers start: 18 outliers final: 14 residues processed: 180 average time/residue: 0.2640 time to fit residues: 61.4772 Evaluate side-chains 185 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8951 Z= 0.220 Angle : 0.533 7.938 12145 Z= 0.276 Chirality : 0.041 0.171 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.240 98.298 1472 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.44 % Allowed : 18.86 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.55 (0.26), residues: 1078 helix: 1.42 (0.27), residues: 396 sheet: -0.35 (0.32), residues: 255 loop : -0.03 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 88 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE D 347 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7875 (t0) cc_final: 0.7315 (t0) REVERT: B 291 ASP cc_start: 0.7649 (t70) cc_final: 0.7158 (t0) REVERT: A 53 MET cc_start: 0.6087 (mpp) cc_final: 0.5562 (mtm) REVERT: D 23 MET cc_start: 0.7734 (mtt) cc_final: 0.7303 (mmp) REVERT: D 74 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7248 (tt) REVERT: D 132 ARG cc_start: 0.8331 (ptm-80) cc_final: 0.7968 (ptp-110) outliers start: 23 outliers final: 19 residues processed: 184 average time/residue: 0.2541 time to fit residues: 61.1849 Evaluate side-chains 192 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8951 Z= 0.169 Angle : 0.528 7.715 12145 Z= 0.272 Chirality : 0.041 0.171 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.166 97.984 1472 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 19.60 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.26), residues: 1078 helix: 1.45 (0.27), residues: 396 sheet: -0.24 (0.32), residues: 253 loop : -0.03 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 88 HIS 0.002 0.001 HIS B 54 PHE 0.017 0.001 PHE D 347 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7829 (t0) cc_final: 0.7253 (t0) REVERT: B 291 ASP cc_start: 0.7617 (t70) cc_final: 0.7123 (t0) REVERT: A 53 MET cc_start: 0.6011 (mpp) cc_final: 0.5760 (ptp) REVERT: D 23 MET cc_start: 0.7720 (mtt) cc_final: 0.7342 (mmp) REVERT: D 74 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7228 (tt) outliers start: 21 outliers final: 16 residues processed: 184 average time/residue: 0.2742 time to fit residues: 65.5452 Evaluate side-chains 183 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 0.0020 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8951 Z= 0.178 Angle : 0.544 8.977 12145 Z= 0.278 Chirality : 0.042 0.221 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.170 98.089 1472 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.80 % Allowed : 20.02 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.26), residues: 1078 helix: 1.45 (0.27), residues: 396 sheet: -0.24 (0.33), residues: 253 loop : -0.03 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.001 PHE D 347 TYR 0.017 0.001 TYR D 130 ARG 0.007 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.083 Fit side-chains REVERT: B 163 ASP cc_start: 0.7812 (t0) cc_final: 0.7252 (t0) REVERT: B 291 ASP cc_start: 0.7613 (t70) cc_final: 0.7119 (t0) REVERT: A 53 MET cc_start: 0.5870 (mpp) cc_final: 0.5648 (ptp) REVERT: D 23 MET cc_start: 0.7720 (mtt) cc_final: 0.7348 (mmp) REVERT: D 74 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7216 (tt) REVERT: D 76 MET cc_start: 0.7717 (mtt) cc_final: 0.7509 (mtp) REVERT: G 13 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5464 (ptp90) outliers start: 17 outliers final: 14 residues processed: 178 average time/residue: 0.2532 time to fit residues: 58.7977 Evaluate side-chains 186 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128384 restraints weight = 11064.938| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.48 r_work: 0.3269 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8951 Z= 0.201 Angle : 0.568 14.594 12145 Z= 0.288 Chirality : 0.043 0.447 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.202 98.198 1472 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.12 % Allowed : 20.13 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.60 (0.26), residues: 1078 helix: 1.45 (0.27), residues: 396 sheet: -0.28 (0.32), residues: 253 loop : -0.02 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.001 PHE D 347 TYR 0.016 0.001 TYR D 130 ARG 0.007 0.001 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.85 seconds wall clock time: 44 minutes 30.00 seconds (2670.00 seconds total)