Starting phenix.real_space_refine on Wed Apr 30 10:09:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k20_36808/04_2025/8k20_36808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k20_36808/04_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_36808/04_2025/8k20_36808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k20_36808/04_2025/8k20_36808.map" model { file = "/net/cci-nas-00/data/ceres_data/8k20_36808/04_2025/8k20_36808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k20_36808/04_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-5669/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: 8.52, per 1000 atoms: 0.91 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.06 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: 2.89 Time building geometry restraints manager: 2.85 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: 8.530 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.860 Find NCS groups from input model: 0.330 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- 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 9509 Z= 0.127 Angle : 0.600 9.152 12865 Z= 0.328 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 Details of bonding type rmsd hydrogen bonds : bond 0.12196 ( 545) hydrogen bonds : angle 5.61877 ( 1569) SS BOND : bond 0.00267 ( 1) SS BOND : angle 5.65363 ( 2) covalent geometry : bond 0.00268 ( 9508) covalent geometry : angle 0.59585 (12863) *********************** 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 : 1.198 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: 0.1901 time to fit residues: 27.5631 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 : 1.186 ------------------------------------------------------------------------------- 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 = 0.087879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072086 restraints weight = 53096.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.073833 restraints weight = 31075.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.075082 restraints weight = 21693.399| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9509 Z= 0.139 Angle : 0.565 7.626 12865 Z= 0.298 Chirality : 0.043 0.160 1508 Planarity : 0.004 0.067 1651 Dihedral : 4.282 20.679 1301 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.29 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 0.019 0.002 TYR C 103 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 545) hydrogen bonds : angle 4.91243 ( 1569) SS BOND : bond 0.00338 ( 1) SS BOND : angle 2.82258 ( 2) covalent geometry : bond 0.00299 ( 9508) covalent geometry : angle 0.56401 (12863) *********************** 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 : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 PHE cc_start: 0.8222 (m-80) cc_final: 0.7825 (m-80) REVERT: C 105 LEU cc_start: 0.6968 (tp) cc_final: 0.6599 (mt) REVERT: C 116 MET cc_start: 0.7089 (mmm) cc_final: 0.6762 (mmm) REVERT: E 276 MET cc_start: 0.7159 (ppp) cc_final: 0.6870 (ppp) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.2188 time to fit residues: 29.2479 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 : 1.201 ------------------------------------------------------------------------------- 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: 0.0470 chunk 90 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.087859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.072418 restraints weight = 53029.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.074283 restraints weight = 33043.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.076409 restraints weight = 20470.858| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9509 Z= 0.125 Angle : 0.536 8.023 12865 Z= 0.281 Chirality : 0.042 0.141 1508 Planarity : 0.004 0.058 1651 Dihedral : 4.182 21.238 1301 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.36 % Allowed : 10.58 % Favored : 88.06 % 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: 0.79 (0.25), residues: 1197 helix: 1.54 (0.21), residues: 613 sheet: -0.72 (0.36), residues: 196 loop : -0.31 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 104 HIS 0.004 0.001 HIS C 75 PHE 0.012 0.001 PHE F 76 TYR 0.014 0.002 TYR C 103 ARG 0.003 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 545) hydrogen bonds : angle 4.72656 ( 1569) SS BOND : bond 0.00420 ( 1) SS BOND : angle 2.54159 ( 2) covalent geometry : bond 0.00267 ( 9508) covalent geometry : angle 0.53535 (12863) *********************** 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 96 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6171 (tp) cc_final: 0.5715 (pt) REVERT: C 17 PHE cc_start: 0.8337 (m-80) cc_final: 0.7919 (m-80) REVERT: C 116 MET cc_start: 0.7288 (mmm) cc_final: 0.7035 (mmm) REVERT: E 5 MET cc_start: 0.2950 (ptm) cc_final: 0.1990 (ptm) REVERT: E 276 MET cc_start: 0.7182 (ppp) cc_final: 0.6920 (ppp) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.2782 time to fit residues: 37.4085 Evaluate side-chains 78 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 5.9990 chunk 103 optimal weight: 0.0010 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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 ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.087014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.070925 restraints weight = 53206.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.072686 restraints weight = 31758.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.073946 restraints weight = 22461.975| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9509 Z= 0.148 Angle : 0.556 8.457 12865 Z= 0.292 Chirality : 0.043 0.149 1508 Planarity : 0.004 0.055 1651 Dihedral : 4.260 20.656 1301 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.75 % Allowed : 13.88 % Favored : 84.37 % 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: 1.48 (0.21), residues: 613 sheet: -1.10 (0.36), residues: 199 loop : -0.37 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 104 HIS 0.004 0.001 HIS E 113 PHE 0.011 0.001 PHE A 208 TYR 0.014 0.002 TYR C 103 ARG 0.003 0.000 ARG F 88 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 545) hydrogen bonds : angle 4.78356 ( 1569) SS BOND : bond 0.00448 ( 1) SS BOND : angle 2.38538 ( 2) covalent geometry : bond 0.00318 ( 9508) covalent geometry : angle 0.55557 (12863) *********************** 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 93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6253 (tp) cc_final: 0.5785 (pt) REVERT: C 17 PHE cc_start: 0.8212 (m-80) cc_final: 0.7796 (m-80) REVERT: C 116 MET cc_start: 0.7376 (mmm) cc_final: 0.7094 (mmm) REVERT: E 5 MET cc_start: 0.3068 (ptm) cc_final: 0.2106 (ptm) outliers start: 18 outliers final: 12 residues processed: 87 average time/residue: 0.1882 time to fit residues: 24.3740 Evaluate side-chains 79 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** B 135 HIS ** 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 = 0.4202 r_free = 0.4202 target = 0.086054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.069846 restraints weight = 53410.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.071585 restraints weight = 32095.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.072795 restraints weight = 22561.633| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9509 Z= 0.178 Angle : 0.595 7.248 12865 Z= 0.315 Chirality : 0.043 0.170 1508 Planarity : 0.004 0.054 1651 Dihedral : 4.437 20.044 1301 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.23 % Allowed : 15.83 % Favored : 81.94 % 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: 609 sheet: -1.14 (0.37), residues: 186 loop : -0.68 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 205 HIS 0.006 0.001 HIS D 30 PHE 0.018 0.002 PHE A 208 TYR 0.015 0.002 TYR E 305 ARG 0.004 0.000 ARG F 88 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 545) hydrogen bonds : angle 4.97085 ( 1569) SS BOND : bond 0.00589 ( 1) SS BOND : angle 2.41122 ( 2) covalent geometry : bond 0.00383 ( 9508) covalent geometry : angle 0.59459 (12863) *********************** 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 97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 TRP cc_start: 0.9124 (p-90) cc_final: 0.8912 (p-90) REVERT: C 17 PHE cc_start: 0.8247 (m-80) cc_final: 0.7806 (m-80) REVERT: E 5 MET cc_start: 0.3125 (ptm) cc_final: 0.2254 (ptm) REVERT: E 299 ASN cc_start: 0.4406 (OUTLIER) cc_final: 0.3207 (t0) REVERT: E 302 MET cc_start: 0.4281 (tpp) cc_final: 0.3720 (tpp) outliers start: 23 outliers final: 11 residues processed: 91 average time/residue: 0.2707 time to fit residues: 36.0375 Evaluate side-chains 80 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 299 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4207 r_free = 0.4207 target = 0.086223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.069999 restraints weight = 53273.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.071751 restraints weight = 32191.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.072958 restraints weight = 22761.334| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9509 Z= 0.155 Angle : 0.579 7.224 12865 Z= 0.305 Chirality : 0.043 0.164 1508 Planarity : 0.003 0.050 1651 Dihedral : 4.425 20.171 1301 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.14 % Allowed : 18.25 % Favored : 79.61 % 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: 0.31 (0.25), residues: 1197 helix: 1.29 (0.21), residues: 609 sheet: -1.15 (0.38), residues: 179 loop : -0.70 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.005 0.001 HIS D 30 PHE 0.012 0.002 PHE A 242 TYR 0.014 0.002 TYR C 103 ARG 0.003 0.000 ARG E 278 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 545) hydrogen bonds : angle 4.93681 ( 1569) SS BOND : bond 0.00285 ( 1) SS BOND : angle 2.74756 ( 2) covalent geometry : bond 0.00336 ( 9508) covalent geometry : angle 0.57850 (12863) *********************** 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 92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6349 (tp) cc_final: 0.5889 (pt) REVERT: C 17 PHE cc_start: 0.8243 (m-80) cc_final: 0.7811 (m-80) REVERT: C 116 MET cc_start: 0.6964 (mmm) cc_final: 0.6685 (mmm) REVERT: E 5 MET cc_start: 0.2924 (ptm) cc_final: 0.2061 (ptm) REVERT: E 100 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3797 (mm) REVERT: E 253 MET cc_start: 0.1903 (tpt) cc_final: 0.1661 (tpt) REVERT: E 299 ASN cc_start: 0.4344 (OUTLIER) cc_final: 0.3228 (t0) REVERT: E 302 MET cc_start: 0.4291 (tpp) cc_final: 0.3650 (tpp) outliers start: 22 outliers final: 14 residues processed: 88 average time/residue: 0.2017 time to fit residues: 26.5112 Evaluate side-chains 82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 C residue 5 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 53 MET 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 299 ASN 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: 0.0980 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4231 r_free = 0.4231 target = 0.087309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.071976 restraints weight = 53438.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.073942 restraints weight = 33308.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.074620 restraints weight = 21163.209| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9509 Z= 0.116 Angle : 0.555 9.499 12865 Z= 0.285 Chirality : 0.043 0.193 1508 Planarity : 0.003 0.050 1651 Dihedral : 4.249 20.124 1301 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.55 % Allowed : 19.32 % Favored : 79.13 % 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: 0.58 (0.25), residues: 1197 helix: 1.53 (0.21), residues: 609 sheet: -1.20 (0.38), residues: 182 loop : -0.50 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 337 HIS 0.005 0.001 HIS F 63 PHE 0.016 0.001 PHE A 242 TYR 0.016 0.001 TYR C 103 ARG 0.002 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 545) hydrogen bonds : angle 4.74107 ( 1569) SS BOND : bond 0.00436 ( 1) SS BOND : angle 2.73727 ( 2) covalent geometry : bond 0.00249 ( 9508) covalent geometry : angle 0.55384 (12863) *********************** 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 93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6247 (tp) cc_final: 0.5816 (pt) REVERT: B 183 MET cc_start: 0.8855 (ppp) cc_final: 0.8642 (ppp) REVERT: C 17 PHE cc_start: 0.8399 (m-80) cc_final: 0.7920 (m-80) REVERT: C 116 MET cc_start: 0.7262 (mmm) cc_final: 0.6925 (mmm) REVERT: E 5 MET cc_start: 0.2719 (ptm) cc_final: 0.1917 (ptm) REVERT: E 100 LEU cc_start: 0.4066 (OUTLIER) cc_final: 0.3631 (mm) REVERT: E 253 MET cc_start: 0.1839 (tpt) cc_final: 0.1571 (tpt) REVERT: E 276 MET cc_start: 0.7509 (ppp) cc_final: 0.6557 (ppp) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.1912 time to fit residues: 25.2061 Evaluate side-chains 82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 291 THR 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 71 THR 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 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 315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 0.0870 chunk 89 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- 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** B 135 HIS B 210 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 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 = 0.4184 r_free = 0.4184 target = 0.085149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.068754 restraints weight = 54488.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.070478 restraints weight = 32854.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.071663 restraints weight = 23191.943| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9509 Z= 0.207 Angle : 0.650 10.042 12865 Z= 0.341 Chirality : 0.045 0.189 1508 Planarity : 0.004 0.048 1651 Dihedral : 4.587 20.217 1301 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.23 % Allowed : 19.42 % Favored : 78.35 % 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: 0.04 (0.25), residues: 1197 helix: 1.19 (0.21), residues: 606 sheet: -1.49 (0.39), residues: 171 loop : -0.91 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 205 HIS 0.008 0.001 HIS D 30 PHE 0.013 0.002 PHE E 10 TYR 0.019 0.002 TYR F 35 ARG 0.003 0.001 ARG E 278 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 545) hydrogen bonds : angle 5.11682 ( 1569) SS BOND : bond 0.00732 ( 1) SS BOND : angle 2.49429 ( 2) covalent geometry : bond 0.00447 ( 9508) covalent geometry : angle 0.64886 (12863) *********************** 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 92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 TRP cc_start: 0.9235 (p-90) cc_final: 0.8951 (p90) REVERT: C 116 MET cc_start: 0.7336 (mmm) cc_final: 0.6964 (mmm) REVERT: E 5 MET cc_start: 0.2872 (ptm) cc_final: 0.2040 (ptm) REVERT: E 100 LEU cc_start: 0.4304 (OUTLIER) cc_final: 0.3854 (mm) REVERT: E 253 MET cc_start: 0.2177 (tpt) cc_final: 0.1901 (tpt) REVERT: E 276 MET cc_start: 0.7659 (ppp) cc_final: 0.6724 (ppp) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.1937 time to fit residues: 24.6634 Evaluate side-chains 85 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 F residue 19 CYS Chi-restraints excluded: chain E residue 19 VAL 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: 0.3980 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4220 r_free = 0.4220 target = 0.086673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.070734 restraints weight = 53176.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.072503 restraints weight = 31493.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.073731 restraints weight = 22065.429| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9509 Z= 0.130 Angle : 0.583 9.208 12865 Z= 0.300 Chirality : 0.044 0.188 1508 Planarity : 0.003 0.048 1651 Dihedral : 4.362 19.790 1301 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.14 % Allowed : 19.32 % 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: 0.32 (0.25), residues: 1197 helix: 1.37 (0.21), residues: 610 sheet: -1.29 (0.40), residues: 168 loop : -0.77 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.004 0.001 HIS F 63 PHE 0.013 0.001 PHE A 242 TYR 0.015 0.001 TYR C 103 ARG 0.002 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 545) hydrogen bonds : angle 4.86320 ( 1569) SS BOND : bond 0.00400 ( 1) SS BOND : angle 2.69134 ( 2) covalent geometry : bond 0.00280 ( 9508) covalent geometry : angle 0.58166 (12863) *********************** 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 93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8169 (t70) cc_final: 0.7730 (t70) REVERT: B 152 LEU cc_start: 0.6226 (tp) cc_final: 0.5808 (pt) REVERT: B 205 TRP cc_start: 0.9185 (p-90) cc_final: 0.8906 (p90) REVERT: C 17 PHE cc_start: 0.8415 (m-80) cc_final: 0.7934 (m-80) REVERT: C 116 MET cc_start: 0.7204 (mmm) cc_final: 0.6787 (mmm) REVERT: D 46 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.8250 (Cg_endo) REVERT: F 17 PHE cc_start: 0.7633 (m-80) cc_final: 0.7414 (m-80) REVERT: E 5 MET cc_start: 0.2862 (ptm) cc_final: 0.2078 (ptm) REVERT: E 100 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.3765 (mm) REVERT: E 276 MET cc_start: 0.7679 (ppp) cc_final: 0.6752 (ppp) outliers start: 22 outliers final: 20 residues processed: 86 average time/residue: 0.2041 time to fit residues: 26.0219 Evaluate side-chains 89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 C residue 71 THR Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 53 MET 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 163 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 317 THR 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: 0.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 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 = 0.4179 r_free = 0.4179 target = 0.084833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.068829 restraints weight = 53925.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.070493 restraints weight = 32328.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.071651 restraints weight = 22755.672| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9509 Z= 0.209 Angle : 0.661 8.827 12865 Z= 0.347 Chirality : 0.045 0.210 1508 Planarity : 0.004 0.044 1651 Dihedral : 4.663 20.139 1301 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.33 % Allowed : 19.42 % 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: -0.06 (0.25), residues: 1197 helix: 1.11 (0.21), residues: 604 sheet: -1.43 (0.41), residues: 159 loop : -1.05 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 205 HIS 0.007 0.001 HIS D 30 PHE 0.018 0.002 PHE A 208 TYR 0.018 0.002 TYR E 305 ARG 0.004 0.001 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 545) hydrogen bonds : angle 5.16812 ( 1569) SS BOND : bond 0.00757 ( 1) SS BOND : angle 2.56787 ( 2) covalent geometry : bond 0.00450 ( 9508) covalent geometry : angle 0.65990 (12863) ********************** 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 92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8211 (t70) cc_final: 0.7799 (t70) REVERT: B 205 TRP cc_start: 0.9244 (p-90) cc_final: 0.8899 (p90) REVERT: C 17 PHE cc_start: 0.8442 (m-80) cc_final: 0.7905 (m-80) REVERT: C 116 MET cc_start: 0.7298 (mmm) cc_final: 0.6974 (mmm) REVERT: E 5 MET cc_start: 0.2865 (ptm) cc_final: 0.2032 (ptm) REVERT: E 100 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.3899 (mm) REVERT: E 253 MET cc_start: 0.2130 (tpt) cc_final: 0.1812 (tpt) REVERT: E 276 MET cc_start: 0.7685 (ppp) cc_final: 0.6761 (ppp) outliers start: 24 outliers final: 21 residues processed: 85 average time/residue: 0.1966 time to fit residues: 24.4817 Evaluate side-chains 90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 C residue 71 THR Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 53 MET 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 163 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 317 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** C 110 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 = 0.4224 r_free = 0.4224 target = 0.086842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.070779 restraints weight = 53242.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.072599 restraints weight = 31515.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.073850 restraints weight = 22020.051| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9509 Z= 0.124 Angle : 0.588 8.866 12865 Z= 0.302 Chirality : 0.044 0.232 1508 Planarity : 0.003 0.049 1651 Dihedral : 4.392 19.918 1301 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.94 % Allowed : 19.81 % 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: 0.35 (0.25), residues: 1197 helix: 1.43 (0.21), residues: 604 sheet: -1.36 (0.40), residues: 168 loop : -0.74 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 337 HIS 0.005 0.001 HIS F 63 PHE 0.013 0.001 PHE A 242 TYR 0.015 0.001 TYR C 103 ARG 0.002 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 545) hydrogen bonds : angle 4.82712 ( 1569) SS BOND : bond 0.00720 ( 1) SS BOND : angle 2.92441 ( 2) covalent geometry : bond 0.00264 ( 9508) covalent geometry : angle 0.58645 (12863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.46 seconds wall clock time: 75 minutes 18.01 seconds (4518.01 seconds total)