Starting phenix.real_space_refine on Thu Mar 13 08:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_42245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_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/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_42245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_42245.map" model { file = "/net/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_42245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uh3_42245/03_2025/8uh3_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. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.38, per 1000 atoms: 0.61 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 - 3.00 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: 2.27 Conformation dependent library (CDL) restraints added in 966.1 milliseconds 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: 0.96 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: 2.43 Time building geometry restraints manager: 2.63 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: 0.00 - 1.52: 11827 1.52 - 3.03: 260 3.03 - 4.55: 41 4.55 - 6.07: 14 6.07 - 7.58: 3 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 3.040 nonbonded pdb=" OD1 ASP D 119 " pdb=" OH TYR D 130 " model vdw 2.199 3.040 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.213 3.120 nonbonded pdb=" NH1 ARG E 202 " pdb=" OE1 GLU E 220 " model vdw 2.218 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.244 3.040 ... (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 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: 1.410 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 1.046 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: 0.2667 time to fit residues: 69.2458 Evaluate side-chains 171 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** E 13 GLN E 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129466 restraints weight = 11025.059| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.49 r_work: 0.3292 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1063 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= 0.186 Angle : 0.527 6.998 12145 Z= 0.277 Chirality : 0.041 0.143 1396 Planarity : 0.004 0.080 1488 Dihedral : 8.251 93.598 1472 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.69 % Allowed : 9.85 % Favored : 88.45 % 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: 0.51 (0.26), residues: 1078 helix: 1.28 (0.26), residues: 396 sheet: -0.38 (0.32), residues: 254 loop : 0.08 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS D 112 PHE 0.010 0.001 PHE A 189 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG B 19 *********************** 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 200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.907 Fit side-chains REVERT: B 163 ASP cc_start: 0.8271 (t0) cc_final: 0.7730 (t0) REVERT: B 189 SER cc_start: 0.8862 (p) cc_final: 0.8657 (p) REVERT: B 214 ARG cc_start: 0.8311 (mmp80) cc_final: 0.8096 (mmt180) REVERT: B 291 ASP cc_start: 0.8251 (t70) cc_final: 0.7798 (t0) REVERT: A 24 ARG cc_start: 0.6930 (ttp-110) cc_final: 0.6705 (ttp-170) REVERT: A 53 MET cc_start: 0.6293 (mpp) cc_final: 0.6076 (mpp) REVERT: A 333 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 337 ASP cc_start: 0.8662 (m-30) cc_final: 0.8373 (m-30) REVERT: D 27 MET cc_start: 0.7904 (ptp) cc_final: 0.7159 (ttt) REVERT: D 215 LYS cc_start: 0.6413 (mmtm) cc_final: 0.5636 (mttp) outliers start: 16 outliers final: 12 residues processed: 189 average time/residue: 0.2857 time to fit residues: 69.8358 Evaluate side-chains 179 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 319 TYR Chi-restraints excluded: chain E residue 5 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN A 195 HIS ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.164681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114937 restraints weight = 11239.985| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.45 r_work: 0.3210 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8951 Z= 0.394 Angle : 0.609 7.235 12145 Z= 0.318 Chirality : 0.044 0.151 1396 Planarity : 0.004 0.079 1488 Dihedral : 8.453 95.348 1472 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.44 % Allowed : 13.35 % Favored : 84.22 % 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: 0.23 (0.26), residues: 1078 helix: 1.22 (0.26), residues: 388 sheet: -0.77 (0.31), residues: 270 loop : -0.02 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS E 167 PHE 0.016 0.002 PHE D 347 TYR 0.020 0.002 TYR E 175 ARG 0.005 0.001 ARG E 202 *********************** 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 201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9009 (m-80) cc_final: 0.8587 (m-80) REVERT: B 105 TYR cc_start: 0.9276 (t80) cc_final: 0.8980 (t80) REVERT: B 291 ASP cc_start: 0.8498 (t70) cc_final: 0.7992 (t0) REVERT: A 24 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6920 (ttp-170) REVERT: A 333 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8244 (tm-30) REVERT: D 23 MET cc_start: 0.8461 (mtt) cc_final: 0.7717 (mmp) REVERT: D 27 MET cc_start: 0.7887 (ptp) cc_final: 0.7202 (ttt) REVERT: D 134 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7914 (ttp-170) outliers start: 23 outliers final: 17 residues processed: 187 average time/residue: 0.3674 time to fit residues: 87.8989 Evaluate side-chains 185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 B residue 331 SER 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 215 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 17 GLU 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 50 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126111 restraints weight = 11055.386| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.55 r_work: 0.3244 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8951 Z= 0.201 Angle : 0.531 6.834 12145 Z= 0.277 Chirality : 0.041 0.179 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.277 96.641 1472 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.44 % Allowed : 15.68 % Favored : 81.89 % 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 (0.27), residues: 388 sheet: -0.59 (0.32), residues: 255 loop : 0.02 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE A 189 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 *********************** 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 204 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.072 Fit side-chains REVERT: B 59 TYR cc_start: 0.8798 (m-80) cc_final: 0.8429 (m-80) REVERT: B 163 ASP cc_start: 0.8174 (t0) cc_final: 0.7531 (t0) REVERT: B 291 ASP cc_start: 0.8303 (t70) cc_final: 0.7774 (t0) REVERT: A 308 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 333 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 23 MET cc_start: 0.8414 (mtt) cc_final: 0.7689 (mmp) REVERT: D 27 MET cc_start: 0.7979 (ptp) cc_final: 0.7263 (ttt) outliers start: 23 outliers final: 17 residues processed: 191 average time/residue: 0.2683 time to fit residues: 66.7354 Evaluate side-chains 192 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 308 GLU 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 176 GLN 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 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 50 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** E 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127527 restraints weight = 11116.805| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.55 r_work: 0.3252 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1494 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= 0.176 Angle : 0.521 6.764 12145 Z= 0.272 Chirality : 0.041 0.145 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.216 97.537 1472 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.44 % Allowed : 16.53 % Favored : 81.04 % 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: 0.52 (0.26), residues: 1078 helix: 1.38 (0.27), residues: 388 sheet: -0.47 (0.32), residues: 254 loop : 0.07 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 88 HIS 0.002 0.001 HIS B 54 PHE 0.015 0.001 PHE A 354 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 *********************** 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 207 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.001 Fit side-chains REVERT: B 59 TYR cc_start: 0.8745 (m-80) cc_final: 0.8422 (m-80) REVERT: B 291 ASP cc_start: 0.8276 (t70) cc_final: 0.7740 (t0) REVERT: A 333 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 23 MET cc_start: 0.8282 (mtt) cc_final: 0.7679 (mmp) REVERT: D 27 MET cc_start: 0.7947 (ptp) cc_final: 0.7198 (ttp) REVERT: D 74 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7358 (tt) REVERT: D 76 MET cc_start: 0.8240 (mtt) cc_final: 0.8036 (mtp) REVERT: D 88 TRP cc_start: 0.6427 (t-100) cc_final: 0.5948 (t-100) REVERT: D 215 LYS cc_start: 0.6460 (mmtm) cc_final: 0.5805 (mttp) outliers start: 23 outliers final: 16 residues processed: 196 average time/residue: 0.2704 time to fit residues: 69.2973 Evaluate side-chains 190 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 234 PHE 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 176 GLN Chi-restraints excluded: chain D residue 179 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123835 restraints weight = 10935.420| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.50 r_work: 0.3202 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1679 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= 0.310 Angle : 0.589 7.405 12145 Z= 0.306 Chirality : 0.043 0.152 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.368 97.768 1472 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.28 % Allowed : 16.95 % Favored : 79.77 % 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: 0.38 (0.26), residues: 1078 helix: 1.26 (0.27), residues: 395 sheet: -0.50 (0.33), residues: 250 loop : -0.07 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.002 PHE E 32 TYR 0.020 0.002 TYR D 130 ARG 0.006 0.001 ARG B 19 *********************** 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 206 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.999 Fit side-chains REVERT: B 59 TYR cc_start: 0.8915 (m-80) cc_final: 0.8490 (m-80) REVERT: B 163 ASP cc_start: 0.8235 (t0) cc_final: 0.7593 (t0) REVERT: B 262 MET cc_start: 0.8045 (tpp) cc_final: 0.7838 (mmt) REVERT: B 291 ASP cc_start: 0.8296 (t70) cc_final: 0.7774 (t0) REVERT: A 333 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8157 (tm-30) REVERT: D 23 MET cc_start: 0.8285 (mtt) cc_final: 0.7684 (mmp) REVERT: D 27 MET cc_start: 0.7905 (ptp) cc_final: 0.7163 (ttp) REVERT: D 74 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7427 (tt) REVERT: D 132 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.7863 (ptp-110) REVERT: D 215 LYS cc_start: 0.6410 (mmtm) cc_final: 0.5811 (mttp) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.2848 time to fit residues: 69.5932 Evaluate side-chains 191 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 234 PHE 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 105 CYS 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 83 MET 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 27 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121248 restraints weight = 11033.119| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.40 r_work: 0.3254 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1703 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= 0.181 Angle : 0.540 7.029 12145 Z= 0.281 Chirality : 0.041 0.152 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.200 97.569 1472 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.65 % Allowed : 18.22 % Favored : 79.13 % 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: 0.52 (0.26), residues: 1078 helix: 1.42 (0.27), residues: 388 sheet: -0.31 (0.33), residues: 246 loop : -0.10 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.017 0.001 PHE A 354 TYR 0.017 0.001 TYR D 130 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 203 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.944 Fit side-chains REVERT: B 59 TYR cc_start: 0.8808 (m-80) cc_final: 0.8422 (m-80) REVERT: B 291 ASP cc_start: 0.8284 (t70) cc_final: 0.7750 (t0) REVERT: A 333 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 23 MET cc_start: 0.8271 (mtt) cc_final: 0.7620 (mmp) REVERT: D 27 MET cc_start: 0.7897 (ptp) cc_final: 0.7228 (ttp) REVERT: D 74 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7331 (tt) REVERT: D 88 TRP cc_start: 0.6383 (t-100) cc_final: 0.5825 (t-100) REVERT: D 130 TYR cc_start: 0.8087 (t80) cc_final: 0.7853 (t80) REVERT: D 132 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.7852 (ptp-110) REVERT: D 215 LYS cc_start: 0.6433 (mmtm) cc_final: 0.5767 (mttp) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.2587 time to fit residues: 64.0303 Evaluate side-chains 195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 234 PHE 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 37 THR 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 155 MET 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 83 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127743 restraints weight = 11148.471| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.45 r_work: 0.3257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8951 Z= 0.201 Angle : 0.554 7.201 12145 Z= 0.287 Chirality : 0.042 0.166 1396 Planarity : 0.004 0.076 1488 Dihedral : 8.219 97.802 1472 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.44 % Allowed : 18.33 % Favored : 79.24 % 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: 0.52 (0.26), residues: 1078 helix: 1.40 (0.27), residues: 388 sheet: -0.30 (0.34), residues: 247 loop : -0.07 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 160 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.001 ARG B 19 *********************** 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 201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.987 Fit side-chains REVERT: B 32 GLN cc_start: 0.8834 (pt0) cc_final: 0.8491 (pt0) REVERT: B 59 TYR cc_start: 0.8914 (m-80) cc_final: 0.8530 (m-80) REVERT: B 137 ARG cc_start: 0.8796 (tpp-160) cc_final: 0.8546 (tpp80) REVERT: B 189 SER cc_start: 0.8903 (p) cc_final: 0.8694 (p) REVERT: B 291 ASP cc_start: 0.8515 (t70) cc_final: 0.8006 (t0) REVERT: A 308 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 333 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 23 MET cc_start: 0.8214 (mtt) cc_final: 0.7592 (mmp) REVERT: D 27 MET cc_start: 0.8045 (ptp) cc_final: 0.7250 (ttp) REVERT: D 74 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7371 (tt) REVERT: D 88 TRP cc_start: 0.6451 (t-100) cc_final: 0.5829 (t-100) REVERT: D 132 ARG cc_start: 0.8659 (ptm-80) cc_final: 0.7879 (ptp-110) REVERT: D 215 LYS cc_start: 0.6472 (mmtm) cc_final: 0.5779 (mttp) outliers start: 23 outliers final: 19 residues processed: 188 average time/residue: 0.2706 time to fit residues: 66.0259 Evaluate side-chains 195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 308 GLU 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 155 MET 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 83 MET 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 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 48 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN A 256 ASN E 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114077 restraints weight = 11277.189| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.39 r_work: 0.3205 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8951 Z= 0.419 Angle : 0.651 7.628 12145 Z= 0.337 Chirality : 0.046 0.233 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.532 98.069 1472 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.75 % Allowed : 17.69 % Favored : 79.56 % 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: 0.19 (0.26), residues: 1078 helix: 1.13 (0.26), residues: 395 sheet: -0.78 (0.32), residues: 269 loop : -0.03 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.004 0.001 HIS E 167 PHE 0.023 0.002 PHE A 354 TYR 0.024 0.002 TYR D 130 ARG 0.006 0.001 ARG B 19 *********************** 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 202 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.555 Fit side-chains REVERT: B 32 GLN cc_start: 0.8905 (pt0) cc_final: 0.8568 (pt0) REVERT: B 59 TYR cc_start: 0.9006 (m-80) cc_final: 0.8609 (m-80) REVERT: B 163 ASP cc_start: 0.8441 (t0) cc_final: 0.7815 (t0) REVERT: B 291 ASP cc_start: 0.8552 (t70) cc_final: 0.8076 (t0) REVERT: A 308 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 333 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8185 (tm-30) REVERT: D 23 MET cc_start: 0.8251 (mtt) cc_final: 0.7599 (mmp) REVERT: D 27 MET cc_start: 0.7976 (ptp) cc_final: 0.7233 (ttp) REVERT: D 74 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7598 (tt) REVERT: D 76 MET cc_start: 0.8426 (mtt) cc_final: 0.8218 (mtp) REVERT: D 130 TYR cc_start: 0.8065 (t80) cc_final: 0.7651 (t80) REVERT: D 132 ARG cc_start: 0.8667 (ptm-80) cc_final: 0.7858 (ptp-110) REVERT: G 20 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8554 (ptpp) outliers start: 26 outliers final: 20 residues processed: 188 average time/residue: 0.3138 time to fit residues: 78.5069 Evaluate side-chains 195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL 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 B residue 271 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 308 GLU 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 155 MET Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123234 restraints weight = 11330.075| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.65 r_work: 0.3206 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.188 8951 Z= 0.343 Angle : 0.934 59.199 12145 Z= 0.535 Chirality : 0.046 0.455 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.567 97.989 1472 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.75 % Allowed : 18.22 % Favored : 79.03 % 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: 0.12 (0.26), residues: 1078 helix: 1.11 (0.26), residues: 396 sheet: -0.81 (0.32), residues: 269 loop : -0.11 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 160 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.002 PHE A 354 TYR 0.021 0.002 TYR D 130 ARG 0.005 0.001 ARG E 160 ********************** 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 200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.931 Fit side-chains REVERT: B 32 GLN cc_start: 0.8826 (pt0) cc_final: 0.8493 (pt0) REVERT: B 59 TYR cc_start: 0.8893 (m-80) cc_final: 0.8524 (m-80) REVERT: B 137 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8406 (tpp80) REVERT: B 163 ASP cc_start: 0.8228 (t0) cc_final: 0.7599 (t0) REVERT: B 291 ASP cc_start: 0.8313 (t70) cc_final: 0.7811 (t0) REVERT: A 308 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: A 333 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8083 (tm-30) REVERT: D 23 MET cc_start: 0.8227 (mtt) cc_final: 0.7591 (mmp) REVERT: D 27 MET cc_start: 0.7918 (ptp) cc_final: 0.7196 (ttp) REVERT: D 74 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7511 (tt) REVERT: D 76 MET cc_start: 0.8391 (mtt) cc_final: 0.8184 (mtp) REVERT: D 130 TYR cc_start: 0.8058 (t80) cc_final: 0.7570 (t80) REVERT: D 132 ARG cc_start: 0.8608 (ptm-80) cc_final: 0.7862 (ptp-110) outliers start: 26 outliers final: 22 residues processed: 187 average time/residue: 0.2579 time to fit residues: 63.2740 Evaluate side-chains 195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL 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 B residue 271 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain D residue 37 THR 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 155 MET 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 13 GLN Chi-restraints excluded: chain E residue 83 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115671 restraints weight = 11358.352| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.51 r_work: 0.3184 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.188 8951 Z= 0.343 Angle : 0.934 59.200 12145 Z= 0.535 Chirality : 0.046 0.455 1396 Planarity : 0.004 0.075 1488 Dihedral : 8.567 97.989 1472 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.54 % Allowed : 18.22 % Favored : 79.24 % 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: 0.12 (0.26), residues: 1078 helix: 1.11 (0.26), residues: 396 sheet: -0.81 (0.32), residues: 269 loop : -0.11 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 160 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.002 PHE A 354 TYR 0.021 0.002 TYR D 130 ARG 0.005 0.001 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.44 seconds wall clock time: 90 minutes 2.67 seconds (5402.67 seconds total)