Starting phenix.real_space_refine on Thu Feb 13 21:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.map" model { file = "/net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k20_36808/02_2025/8k20_36808.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 55 5.16 5 C 5899 2.51 5 N 1618 2.21 5 O 1783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9356 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2596 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1618 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "C" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1312 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Chain: "D" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 609 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "E" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2596 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.75, per 1000 atoms: 0.83 Number of scatterers: 9356 At special positions: 0 Unit cell: (85.14, 96.32, 159.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 55 16.00 O 1783 8.00 N 1618 7.00 C 5899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 19 " distance=2.03 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: 2.09 Conformation dependent library (CDL) restraints added in 998.4 milliseconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 14 sheets defined 55.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 69 removed outlier: 4.924A pdb=" N LEU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.757A pdb=" N LEU A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 208 through 225 removed outlier: 4.060A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 257 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 299 through 314 removed outlier: 4.443A pdb=" N ILE A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.924A pdb=" N GLU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'B' and resid 45 through 70 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.897A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 183 removed outlier: 3.809A pdb=" N LYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 4.632A pdb=" N CYS B 187 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 221 removed outlier: 3.671A pdb=" N THR B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 49 through 66 removed outlier: 4.198A pdb=" N LEU C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 removed outlier: 3.626A pdb=" N SER C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 84 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 157 through 169 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'D' and resid 27 through 40 removed outlier: 3.734A pdb=" N ALA D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 93 Processing helix chain 'F' and resid 27 through 39 removed outlier: 3.674A pdb=" N ALA F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 91 Processing helix chain 'E' and resid 45 through 69 removed outlier: 4.593A pdb=" N LEU E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 86 through 105 Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 160 through 172 Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 208 through 226 Processing helix chain 'E' and resid 229 through 257 removed outlier: 3.611A pdb=" N LEU E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 269 Processing helix chain 'E' and resid 270 through 284 removed outlier: 4.122A pdb=" N GLN E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.516A pdb=" N ILE E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.862A pdb=" N ILE E 303 " --> pdb=" O ASN E 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR E 306 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 removed outlier: 3.856A pdb=" N SER E 322 " --> pdb=" O ILE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.224A pdb=" N ILE A 21 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.224A pdb=" N ILE A 21 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 8 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR A 81 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 10 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY A 83 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 78 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 111 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR A 80 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 155 removed outlier: 6.464A pdb=" N VAL A 142 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 155 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR A 140 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 131 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL A 264 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 133 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 261 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.607A pdb=" N LYS B 16 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER B 86 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 80 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 88 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.605A pdb=" N ALA C 107 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 40 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.077A pdb=" N LEU C 16 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 21 Processing sheet with id=AB1, first strand: chain 'F' and resid 17 through 21 Processing sheet with id=AB2, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.199A pdb=" N ILE E 21 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.199A pdb=" N ILE E 21 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 22 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA E 7 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE E 6 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE E 78 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE E 8 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR E 80 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE E 10 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS E 82 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 149 through 155 removed outlier: 5.065A pdb=" N TYR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER E 146 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE E 152 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA E 144 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 154 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 131 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL E 264 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU E 133 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 202 549 hydrogen bonds defined for protein. 1569 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: 2.63 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3131 1.35 - 1.47: 2075 1.47 - 1.59: 4219 1.59 - 1.72: 0 1.72 - 1.84: 83 Bond restraints: 9508 Sorted by residual: bond pdb=" CB PRO D 46 " pdb=" CG PRO D 46 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 bond pdb=" CG PRO D 46 " pdb=" CD PRO D 46 " ideal model delta sigma weight residual 1.503 1.455 0.048 3.40e-02 8.65e+02 1.97e+00 bond pdb=" CB ARG A 167 " pdb=" CG ARG A 167 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.16e-01 bond pdb=" CB CYS F 19 " pdb=" SG CYS F 19 " ideal model delta sigma weight residual 1.808 1.837 -0.029 3.30e-02 9.18e+02 7.85e-01 bond pdb=" CB MET E 302 " pdb=" CG MET E 302 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.09e-01 ... (remaining 9503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12637 1.83 - 3.66: 189 3.66 - 5.49: 28 5.49 - 7.32: 8 7.32 - 9.15: 1 Bond angle restraints: 12863 Sorted by residual: angle pdb=" N VAL E 336 " pdb=" CA VAL E 336 " pdb=" C VAL E 336 " ideal model delta sigma weight residual 113.71 109.48 4.23 9.50e-01 1.11e+00 1.99e+01 angle pdb=" CG ARG A 167 " pdb=" CD ARG A 167 " pdb=" NE ARG A 167 " ideal model delta sigma weight residual 112.00 121.15 -9.15 2.20e+00 2.07e-01 1.73e+01 angle pdb=" CA PRO D 46 " pdb=" N PRO D 46 " pdb=" CD PRO D 46 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.18e+01 angle pdb=" C CYS D 19 " pdb=" CA CYS D 19 " pdb=" CB CYS D 19 " ideal model delta sigma weight residual 111.78 105.76 6.02 1.98e+00 2.55e-01 9.23e+00 angle pdb=" C ASP A 166 " pdb=" N ARG A 167 " pdb=" CA ARG A 167 " ideal model delta sigma weight residual 121.14 115.92 5.22 1.75e+00 3.27e-01 8.91e+00 ... (remaining 12858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 5037 15.38 - 30.76: 574 30.76 - 46.14: 124 46.14 - 61.52: 29 61.52 - 76.90: 11 Dihedral angle restraints: 5775 sinusoidal: 2279 harmonic: 3496 Sorted by residual: dihedral pdb=" CA SER D 18 " pdb=" C SER D 18 " pdb=" N CYS D 19 " pdb=" CA CYS D 19 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA TYR C 103 " pdb=" C TYR C 103 " pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta harmonic sigma weight residual 180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG A 167 " pdb=" C ARG A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1090 0.042 - 0.085: 323 0.085 - 0.127: 82 0.127 - 0.169: 9 0.169 - 0.211: 4 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CB ILE A 37 " pdb=" CA ILE A 37 " pdb=" CG1 ILE A 37 " pdb=" CG2 ILE A 37 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU F 21 " pdb=" CB LEU F 21 " pdb=" CD1 LEU F 21 " pdb=" CD2 LEU F 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB ILE A 17 " pdb=" CA ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CG2 ILE A 17 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 1505 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 45 " -0.072 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO D 46 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 46 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 46 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 45 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO F 46 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 46 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 46 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 273 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C LEU E 273 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU E 273 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN E 274 " -0.013 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 183 2.66 - 3.22: 9191 3.22 - 3.78: 15442 3.78 - 4.34: 19622 4.34 - 4.90: 31867 Nonbonded interactions: 76305 Sorted by model distance: nonbonded pdb=" OD2 ASP A 298 " pdb="FE FE A 401 " model vdw 2.100 2.260 nonbonded pdb=" OG SER C 98 " pdb=" OD1 ASN C 100 " model vdw 2.160 3.040 nonbonded pdb=" O LEU A 24 " pdb=" OH TYR A 305 " model vdw 2.224 3.040 nonbonded pdb=" N ASP F 16 " pdb=" OE2 GLU F 65 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR E 23 " pdb=" OD1 ASP E 25 " model vdw 2.240 3.040 ... (remaining 76300 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 339) selection = (chain 'E' and resid 4 through 339) } ncs_group { reference = (chain 'D' and resid 16 through 92) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.410 Find NCS groups from input model: 0.290 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 0.075 9508 Z= 0.165 Angle : 0.596 9.152 12863 Z= 0.326 Chirality : 0.043 0.211 1508 Planarity : 0.005 0.106 1651 Dihedral : 14.078 76.901 3512 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.88 (0.24), residues: 1197 helix: 1.67 (0.21), residues: 594 sheet: -0.45 (0.37), residues: 189 loop : -0.40 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 104 HIS 0.004 0.001 HIS A 52 PHE 0.017 0.001 PHE F 76 TYR 0.018 0.001 TYR C 103 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.4952 (m-10) cc_final: 0.4701 (m100) REVERT: B 208 THR cc_start: 0.9039 (p) cc_final: 0.8563 (p) REVERT: C 17 PHE cc_start: 0.8463 (m-80) cc_final: 0.7946 (m-80) REVERT: C 105 LEU cc_start: 0.7598 (tp) cc_final: 0.7050 (mt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1863 time to fit residues: 26.9653 Evaluate side-chains 75 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN E 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.087886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072096 restraints weight = 53101.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.073853 restraints weight = 31046.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.075090 restraints weight = 21665.438| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9508 Z= 0.197 Angle : 0.564 7.629 12863 Z= 0.298 Chirality : 0.043 0.160 1508 Planarity : 0.004 0.067 1651 Dihedral : 4.282 20.683 1301 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.68 % Allowed : 6.80 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.71 (0.25), residues: 1197 helix: 1.50 (0.21), residues: 612 sheet: -0.73 (0.35), residues: 205 loop : -0.39 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 104 HIS 0.005 0.001 HIS C 75 PHE 0.016 0.001 PHE F 76 TYR 0.018 0.002 TYR C 103 ARG 0.004 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 PHE cc_start: 0.8231 (m-80) cc_final: 0.7831 (m-80) REVERT: C 105 LEU cc_start: 0.6971 (tp) cc_final: 0.6603 (mt) REVERT: C 116 MET cc_start: 0.7094 (mmm) cc_final: 0.6767 (mmm) REVERT: E 276 MET cc_start: 0.7162 (ppp) cc_final: 0.6871 (ppp) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1999 time to fit residues: 26.6757 Evaluate side-chains 79 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain D residue 19 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.0030 chunk 90 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** 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 = 0.4232 r_free = 0.4232 target = 0.087746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.071871 restraints weight = 52937.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.073708 restraints weight = 31150.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.075000 restraints weight = 21635.294| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9508 Z= 0.182 Angle : 0.537 7.839 12863 Z= 0.282 Chirality : 0.042 0.140 1508 Planarity : 0.004 0.058 1651 Dihedral : 4.207 21.178 1301 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.36 % Allowed : 10.68 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.78 (0.25), residues: 1197 helix: 1.53 (0.21), residues: 613 sheet: -0.69 (0.36), residues: 195 loop : -0.34 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 104 HIS 0.004 0.001 HIS C 75 PHE 0.012 0.001 PHE F 76 TYR 0.015 0.002 TYR C 103 ARG 0.003 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7381 (pmm) cc_final: 0.7063 (pmm) REVERT: B 152 LEU cc_start: 0.6188 (tp) cc_final: 0.5725 (pt) REVERT: C 17 PHE cc_start: 0.8141 (m-80) cc_final: 0.7787 (m-80) REVERT: C 116 MET cc_start: 0.7336 (mmm) cc_final: 0.7079 (mmm) REVERT: E 5 MET cc_start: 0.2930 (ptm) cc_final: 0.1968 (ptm) REVERT: E 276 MET cc_start: 0.7151 (ppp) cc_final: 0.6876 (ppp) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.2089 time to fit residues: 27.8455 Evaluate side-chains 77 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 53 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS E 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.084905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.068666 restraints weight = 53872.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.070372 restraints weight = 32789.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.071573 restraints weight = 23212.830| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9508 Z= 0.337 Angle : 0.670 8.226 12863 Z= 0.358 Chirality : 0.046 0.196 1508 Planarity : 0.004 0.056 1651 Dihedral : 4.756 22.093 1301 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.62 % Allowed : 14.17 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.00 (0.25), residues: 1197 helix: 1.01 (0.21), residues: 609 sheet: -1.25 (0.38), residues: 182 loop : -0.79 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 104 HIS 0.009 0.002 HIS E 113 PHE 0.025 0.002 PHE A 208 TYR 0.021 0.002 TYR E 305 ARG 0.009 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8105 (t70) cc_final: 0.7711 (t70) REVERT: C 17 PHE cc_start: 0.8218 (m-80) cc_final: 0.7754 (m-80) REVERT: C 116 MET cc_start: 0.7394 (mmm) cc_final: 0.7113 (mmm) REVERT: E 5 MET cc_start: 0.3373 (ptm) cc_final: 0.2430 (ptm) REVERT: E 276 MET cc_start: 0.7199 (ppp) cc_final: 0.6999 (ppp) REVERT: E 299 ASN cc_start: 0.4579 (OUTLIER) cc_final: 0.3089 (t0) REVERT: E 302 MET cc_start: 0.4333 (tpp) cc_final: 0.3845 (tpp) outliers start: 27 outliers final: 16 residues processed: 90 average time/residue: 0.1773 time to fit residues: 24.3373 Evaluate side-chains 81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 299 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4214 r_free = 0.4214 target = 0.086529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.070485 restraints weight = 54029.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072186 restraints weight = 32448.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.073376 restraints weight = 22744.456| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9508 Z= 0.200 Angle : 0.569 6.744 12863 Z= 0.298 Chirality : 0.043 0.173 1508 Planarity : 0.004 0.051 1651 Dihedral : 4.475 20.056 1301 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.84 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.32 (0.25), residues: 1197 helix: 1.30 (0.21), residues: 606 sheet: -1.17 (0.38), residues: 182 loop : -0.67 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 205 HIS 0.004 0.001 HIS C 75 PHE 0.009 0.001 PHE B 209 TYR 0.015 0.002 TYR C 103 ARG 0.002 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6299 (tp) cc_final: 0.5857 (pt) REVERT: C 17 PHE cc_start: 0.8224 (m-80) cc_final: 0.7792 (m-80) REVERT: C 116 MET cc_start: 0.7351 (mmm) cc_final: 0.6991 (mmp) REVERT: E 5 MET cc_start: 0.2884 (ptm) cc_final: 0.1992 (ptm) REVERT: E 100 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3731 (mm) outliers start: 19 outliers final: 8 residues processed: 85 average time/residue: 0.1870 time to fit residues: 24.1659 Evaluate side-chains 73 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.086672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.070637 restraints weight = 53563.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.072397 restraints weight = 31999.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.073618 restraints weight = 22500.318| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9508 Z= 0.192 Angle : 0.575 8.865 12863 Z= 0.300 Chirality : 0.043 0.156 1508 Planarity : 0.003 0.051 1651 Dihedral : 4.416 20.209 1301 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.04 % Allowed : 19.22 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.37 (0.25), residues: 1197 helix: 1.33 (0.21), residues: 608 sheet: -1.13 (0.38), residues: 180 loop : -0.62 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.004 0.001 HIS F 63 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR C 103 ARG 0.003 0.000 ARG E 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6308 (tp) cc_final: 0.5864 (pt) REVERT: C 17 PHE cc_start: 0.8224 (m-80) cc_final: 0.7767 (m-80) REVERT: C 116 MET cc_start: 0.7393 (mmm) cc_final: 0.7037 (mmp) REVERT: E 5 MET cc_start: 0.2920 (ptm) cc_final: 0.2089 (ptm) REVERT: E 100 LEU cc_start: 0.4129 (OUTLIER) cc_final: 0.3713 (mm) REVERT: E 253 MET cc_start: 0.1828 (tpt) cc_final: 0.1594 (tpt) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1818 time to fit residues: 23.1408 Evaluate side-chains 78 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 80 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4228 r_free = 0.4228 target = 0.087117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.071274 restraints weight = 54171.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.073003 restraints weight = 32112.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.074215 restraints weight = 22550.946| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9508 Z= 0.171 Angle : 0.559 7.773 12863 Z= 0.291 Chirality : 0.043 0.198 1508 Planarity : 0.003 0.049 1651 Dihedral : 4.314 20.106 1301 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.23 % Allowed : 19.22 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.25), residues: 1197 helix: 1.46 (0.21), residues: 608 sheet: -1.08 (0.39), residues: 180 loop : -0.58 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 205 HIS 0.005 0.001 HIS F 63 PHE 0.015 0.001 PHE A 242 TYR 0.015 0.001 TYR C 103 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8134 (t70) cc_final: 0.7740 (t70) REVERT: B 152 LEU cc_start: 0.6257 (tp) cc_final: 0.5834 (pt) REVERT: B 183 MET cc_start: 0.8820 (ppp) cc_final: 0.8532 (ppp) REVERT: C 17 PHE cc_start: 0.8176 (m-80) cc_final: 0.7728 (m-80) REVERT: C 116 MET cc_start: 0.7385 (mmm) cc_final: 0.7044 (mmp) REVERT: E 5 MET cc_start: 0.2906 (ptm) cc_final: 0.2108 (ptm) REVERT: E 100 LEU cc_start: 0.4123 (OUTLIER) cc_final: 0.3700 (mm) REVERT: E 253 MET cc_start: 0.1738 (tpt) cc_final: 0.1506 (tpt) REVERT: E 276 MET cc_start: 0.7451 (ppp) cc_final: 0.6564 (ppp) REVERT: E 299 ASN cc_start: 0.4265 (OUTLIER) cc_final: 0.3293 (t0) REVERT: E 302 MET cc_start: 0.4414 (tpp) cc_final: 0.3869 (tpp) outliers start: 23 outliers final: 15 residues processed: 92 average time/residue: 0.1804 time to fit residues: 25.3062 Evaluate side-chains 83 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.087481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.071425 restraints weight = 54355.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.073232 restraints weight = 32455.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.074512 restraints weight = 22665.360| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9508 Z= 0.163 Angle : 0.570 10.968 12863 Z= 0.291 Chirality : 0.045 0.459 1508 Planarity : 0.003 0.049 1651 Dihedral : 4.237 20.130 1301 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.43 % Allowed : 19.32 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.25), residues: 1197 helix: 1.52 (0.21), residues: 609 sheet: -1.05 (0.39), residues: 181 loop : -0.52 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 205 HIS 0.005 0.001 HIS F 63 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR C 103 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6226 (tp) cc_final: 0.5807 (pt) REVERT: B 183 MET cc_start: 0.8860 (ppp) cc_final: 0.8632 (ppp) REVERT: C 17 PHE cc_start: 0.8184 (m-80) cc_final: 0.7799 (m-80) REVERT: C 116 MET cc_start: 0.7355 (mmm) cc_final: 0.7029 (mmp) REVERT: F 17 PHE cc_start: 0.7637 (m-80) cc_final: 0.7411 (m-80) REVERT: E 5 MET cc_start: 0.2783 (ptm) cc_final: 0.2016 (ptm) REVERT: E 100 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.3648 (mm) REVERT: E 253 MET cc_start: 0.1748 (tpt) cc_final: 0.1510 (tpt) REVERT: E 276 MET cc_start: 0.7556 (ppp) cc_final: 0.6653 (ppp) REVERT: E 299 ASN cc_start: 0.4085 (OUTLIER) cc_final: 0.3229 (t0) REVERT: E 302 MET cc_start: 0.4378 (tpp) cc_final: 0.3820 (tpp) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.1957 time to fit residues: 26.8693 Evaluate side-chains 86 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 315 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN C 10 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.087545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.071701 restraints weight = 53834.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.073417 restraints weight = 31853.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.074609 restraints weight = 22243.506| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9508 Z= 0.167 Angle : 0.571 8.912 12863 Z= 0.293 Chirality : 0.044 0.406 1508 Planarity : 0.003 0.046 1651 Dihedral : 4.175 20.267 1301 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.04 % Allowed : 19.71 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.69 (0.25), residues: 1197 helix: 1.59 (0.21), residues: 604 sheet: -1.07 (0.39), residues: 181 loop : -0.42 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.005 0.001 HIS F 63 PHE 0.013 0.001 PHE A 242 TYR 0.016 0.001 TYR C 103 ARG 0.002 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7509 (pmm) cc_final: 0.6767 (pmm) REVERT: A 166 ASP cc_start: 0.8135 (t70) cc_final: 0.7717 (t70) REVERT: B 183 MET cc_start: 0.8884 (ppp) cc_final: 0.8671 (ppp) REVERT: C 17 PHE cc_start: 0.8242 (m-80) cc_final: 0.7831 (m-80) REVERT: C 116 MET cc_start: 0.7348 (mmm) cc_final: 0.7027 (mmp) REVERT: F 17 PHE cc_start: 0.7625 (m-80) cc_final: 0.7401 (m-80) REVERT: E 5 MET cc_start: 0.2798 (ptm) cc_final: 0.2037 (ptm) REVERT: E 100 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3750 (mm) REVERT: E 253 MET cc_start: 0.1747 (tpt) cc_final: 0.1507 (tpt) REVERT: E 276 MET cc_start: 0.7539 (ppp) cc_final: 0.6435 (ppp) REVERT: E 280 MET cc_start: 0.8562 (mpp) cc_final: 0.8289 (mpp) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.2119 time to fit residues: 28.0757 Evaluate side-chains 89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 94 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 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 = 0.4206 r_free = 0.4206 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.069858 restraints weight = 54423.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.071621 restraints weight = 32442.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.072826 restraints weight = 22778.504| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9508 Z= 0.232 Angle : 0.622 10.025 12863 Z= 0.322 Chirality : 0.045 0.379 1508 Planarity : 0.003 0.042 1651 Dihedral : 4.385 20.146 1301 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.04 % Allowed : 19.90 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.30 (0.25), residues: 1197 helix: 1.31 (0.21), residues: 608 sheet: -1.11 (0.40), residues: 168 loop : -0.78 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 205 HIS 0.005 0.001 HIS E 113 PHE 0.011 0.002 PHE E 10 TYR 0.017 0.002 TYR F 35 ARG 0.004 0.000 ARG D 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.7587 (pmm) cc_final: 0.6809 (pmm) REVERT: B 183 MET cc_start: 0.8886 (ppp) cc_final: 0.8640 (ppp) REVERT: C 17 PHE cc_start: 0.8170 (m-80) cc_final: 0.7734 (m-80) REVERT: F 17 PHE cc_start: 0.7734 (m-80) cc_final: 0.7483 (m-80) REVERT: E 5 MET cc_start: 0.2897 (ptm) cc_final: 0.2133 (ptm) REVERT: E 100 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3796 (mm) REVERT: E 253 MET cc_start: 0.1952 (tpt) cc_final: 0.1684 (tpt) REVERT: E 276 MET cc_start: 0.7558 (ppp) cc_final: 0.6445 (ppp) REVERT: E 280 MET cc_start: 0.8621 (mpp) cc_final: 0.8330 (mpp) REVERT: E 302 MET cc_start: 0.4574 (tpp) cc_final: 0.4229 (tpp) outliers start: 21 outliers final: 18 residues processed: 83 average time/residue: 0.1838 time to fit residues: 23.3797 Evaluate side-chains 86 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 114 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 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 = 0.4226 r_free = 0.4226 target = 0.086998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.070950 restraints weight = 54384.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.072724 restraints weight = 32429.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.073952 restraints weight = 22787.317| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9508 Z= 0.175 Angle : 0.586 8.965 12863 Z= 0.299 Chirality : 0.044 0.335 1508 Planarity : 0.003 0.044 1651 Dihedral : 4.280 20.252 1301 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 20.10 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.49 (0.25), residues: 1197 helix: 1.48 (0.21), residues: 602 sheet: -1.13 (0.40), residues: 166 loop : -0.64 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.004 0.001 HIS F 63 PHE 0.012 0.001 PHE A 242 TYR 0.014 0.001 TYR C 103 ARG 0.002 0.000 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.95 seconds wall clock time: 66 minutes 40.72 seconds (4000.72 seconds total)