Starting phenix.real_space_refine on Sun Dec 29 00:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k20_36808/12_2024/8k20_36808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k20_36808/12_2024/8k20_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_36808/12_2024/8k20_36808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k20_36808/12_2024/8k20_36808.map" model { file = "/net/cci-nas-00/data/ceres_data/8k20_36808/12_2024/8k20_36808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k20_36808/12_2024/8k20_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.96, per 1000 atoms: 0.85 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 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: 1.23 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: 2.83 Time building geometry restraints manager: 2.64 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: 9.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.440 Find NCS groups from input model: 0.290 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- 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 : 1.111 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: 0.1937 time to fit residues: 27.9303 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 : 1.109 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 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 : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 PHE cc_start: 0.8446 (m-80) cc_final: 0.7988 (m-80) REVERT: C 105 LEU cc_start: 0.7071 (tp) cc_final: 0.6692 (mt) REVERT: C 116 MET cc_start: 0.7217 (mmm) cc_final: 0.6901 (mmm) REVERT: E 276 MET cc_start: 0.7152 (ppp) cc_final: 0.6857 (ppp) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.2061 time to fit residues: 27.6324 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 : 1.187 ------------------------------------------------------------------------------- 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 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.1368 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= 0.200 Angle : 0.548 7.917 12863 Z= 0.289 Chirality : 0.043 0.148 1508 Planarity : 0.004 0.058 1651 Dihedral : 4.255 21.138 1301 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.36 % Allowed : 10.97 % Favored : 87.67 % 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: 1.49 (0.21), residues: 613 sheet: -0.77 (0.36), residues: 195 loop : -0.37 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 F 88 *********************** 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 93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6243 (tp) cc_final: 0.5753 (pt) REVERT: C 17 PHE cc_start: 0.8398 (m-80) cc_final: 0.7955 (m-80) REVERT: C 116 MET cc_start: 0.7390 (mmm) cc_final: 0.7129 (mmm) REVERT: E 5 MET cc_start: 0.2379 (ptm) cc_final: 0.1447 (ptm) REVERT: E 276 MET cc_start: 0.7150 (ppp) cc_final: 0.6883 (ppp) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.2235 time to fit residues: 29.0676 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 : 1.080 ------------------------------------------------------------------------------- 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 105 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS E 274 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9508 Z= 0.280 Angle : 0.619 8.130 12863 Z= 0.329 Chirality : 0.044 0.228 1508 Planarity : 0.004 0.055 1651 Dihedral : 4.579 20.586 1301 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.52 % Allowed : 14.56 % Favored : 82.91 % 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: 0.16 (0.25), residues: 1197 helix: 1.17 (0.21), residues: 611 sheet: -1.28 (0.37), residues: 188 loop : -0.71 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 104 HIS 0.007 0.001 HIS E 113 PHE 0.022 0.002 PHE A 208 TYR 0.017 0.002 TYR E 305 ARG 0.005 0.001 ARG E 278 *********************** 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 99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 PHE cc_start: 0.8440 (m-80) cc_final: 0.7957 (m-80) REVERT: C 116 MET cc_start: 0.7538 (mmm) cc_final: 0.7249 (mmm) REVERT: D 64 PHE cc_start: 0.6875 (t80) cc_final: 0.6605 (t80) REVERT: E 5 MET cc_start: 0.2605 (ptm) cc_final: 0.1701 (ptm) REVERT: E 299 ASN cc_start: 0.4414 (OUTLIER) cc_final: 0.2886 (t0) REVERT: E 302 MET cc_start: 0.3974 (tpp) cc_final: 0.3380 (tpp) outliers start: 26 outliers final: 14 residues processed: 92 average time/residue: 0.1931 time to fit residues: 26.6667 Evaluate side-chains 81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 299 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 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** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.1939 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= 0.194 Angle : 0.564 7.348 12863 Z= 0.295 Chirality : 0.043 0.178 1508 Planarity : 0.003 0.050 1651 Dihedral : 4.410 20.045 1301 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.75 % Allowed : 16.99 % Favored : 81.26 % 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: 0.41 (0.25), residues: 1197 helix: 1.35 (0.21), residues: 610 sheet: -1.13 (0.38), residues: 182 loop : -0.57 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 205 HIS 0.004 0.001 HIS C 75 PHE 0.011 0.001 PHE E 10 TYR 0.015 0.001 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 94 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6326 (tp) cc_final: 0.5870 (pt) REVERT: C 17 PHE cc_start: 0.8408 (m-80) cc_final: 0.7938 (m-80) REVERT: C 116 MET cc_start: 0.7474 (mmm) cc_final: 0.7122 (mmp) REVERT: D 64 PHE cc_start: 0.6631 (t80) cc_final: 0.6417 (t80) REVERT: E 5 MET cc_start: 0.2256 (ptm) cc_final: 0.1435 (ptm) REVERT: E 100 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3760 (mm) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.2150 time to fit residues: 28.3961 Evaluate side-chains 77 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 163 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 0.0570 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 0.0030 overall best weight: 0.8912 ------------------------------------------------------------------------------- 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 ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2061 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= 0.197 Angle : 0.558 6.758 12863 Z= 0.294 Chirality : 0.043 0.160 1508 Planarity : 0.003 0.050 1651 Dihedral : 4.373 20.221 1301 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: 0.45 (0.25), residues: 1197 helix: 1.39 (0.21), residues: 609 sheet: -1.12 (0.38), residues: 180 loop : -0.56 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.004 0.001 HIS C 75 PHE 0.021 0.001 PHE D 79 TYR 0.014 0.001 TYR C 103 ARG 0.002 0.000 ARG F 88 *********************** 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 91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.6350 (tp) cc_final: 0.5888 (pt) REVERT: C 17 PHE cc_start: 0.8415 (m-80) cc_final: 0.7923 (m-80) REVERT: C 116 MET cc_start: 0.7504 (mmm) cc_final: 0.7149 (mmp) REVERT: D 64 PHE cc_start: 0.6610 (t80) cc_final: 0.6395 (t80) REVERT: E 5 MET cc_start: 0.2163 (ptm) cc_final: 0.1362 (ptm) REVERT: E 100 LEU cc_start: 0.4144 (OUTLIER) cc_final: 0.3752 (mm) REVERT: E 253 MET cc_start: 0.1769 (tpt) cc_final: 0.1551 (tpt) REVERT: E 276 MET cc_start: 0.7522 (ppp) cc_final: 0.6674 (ppp) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.2007 time to fit residues: 25.5304 Evaluate side-chains 81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 163 ASN 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 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9508 Z= 0.262 Angle : 0.610 8.891 12863 Z= 0.323 Chirality : 0.044 0.191 1508 Planarity : 0.004 0.048 1651 Dihedral : 4.559 20.039 1301 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.43 % Allowed : 19.71 % Favored : 77.86 % 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: 0.13 (0.25), residues: 1197 helix: 1.24 (0.21), residues: 603 sheet: -1.27 (0.40), residues: 161 loop : -0.93 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 205 HIS 0.006 0.001 HIS E 113 PHE 0.022 0.002 PHE A 208 TYR 0.016 0.002 TYR F 35 ARG 0.003 0.000 ARG F 88 *********************** 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: 25 poor density : 68 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8297 (t70) cc_final: 0.7942 (t70) REVERT: D 64 PHE cc_start: 0.6790 (t80) cc_final: 0.6536 (t80) REVERT: E 5 MET cc_start: 0.2164 (ptm) cc_final: 0.1369 (ptm) REVERT: E 100 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3812 (mm) REVERT: E 253 MET cc_start: 0.1934 (tpt) cc_final: 0.1689 (tpt) REVERT: E 276 MET cc_start: 0.7589 (ppp) cc_final: 0.6680 (ppp) outliers start: 25 outliers final: 18 residues processed: 88 average time/residue: 0.2003 time to fit residues: 26.3673 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 : 1.085 ------------------------------------------------------------------------------- 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 19 CYS Chi-restraints excluded: chain D residue 33 ILE 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 163 ASN 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 67 optimal weight: 0.0270 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2650 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= 0.310 Angle : 0.665 7.712 12863 Z= 0.351 Chirality : 0.046 0.205 1508 Planarity : 0.004 0.046 1651 Dihedral : 4.853 20.249 1301 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.43 % Allowed : 20.10 % Favored : 77.48 % 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: -0.28 (0.25), residues: 1197 helix: 0.98 (0.21), residues: 601 sheet: -1.79 (0.39), residues: 169 loop : -1.07 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 104 HIS 0.007 0.001 HIS D 30 PHE 0.026 0.002 PHE A 208 TYR 0.017 0.002 TYR F 35 ARG 0.004 0.001 ARG E 278 *********************** 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: 25 poor density : 67 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 PHE cc_start: 0.8775 (m-80) cc_final: 0.8086 (m-80) REVERT: E 5 MET cc_start: 0.2200 (ptm) cc_final: 0.1410 (ptm) REVERT: E 100 LEU cc_start: 0.4445 (OUTLIER) cc_final: 0.3931 (mm) REVERT: E 253 MET cc_start: 0.2018 (tpt) cc_final: 0.1784 (tpt) REVERT: E 276 MET cc_start: 0.7900 (ppp) cc_final: 0.7088 (ppp) outliers start: 25 outliers final: 23 residues processed: 86 average time/residue: 0.1964 time to fit residues: 25.1965 Evaluate side-chains 89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 156 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 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 33 ILE 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 163 ASN Chi-restraints excluded: chain E residue 248 ILE 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 98 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9508 Z= 0.188 Angle : 0.595 9.127 12863 Z= 0.307 Chirality : 0.044 0.248 1508 Planarity : 0.003 0.047 1651 Dihedral : 4.544 19.571 1301 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.43 % Allowed : 19.90 % Favored : 77.67 % 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: 0.07 (0.25), residues: 1197 helix: 1.22 (0.21), residues: 605 sheet: -1.62 (0.39), residues: 166 loop : -0.85 (0.31), residues: 426 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 0.010 0.001 PHE E 311 TYR 0.016 0.001 TYR C 103 ARG 0.002 0.000 ARG E 272 *********************** 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 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8284 (t70) cc_final: 0.7894 (t70) REVERT: C 17 PHE cc_start: 0.8745 (m-80) cc_final: 0.8114 (m-80) REVERT: D 46 PRO cc_start: 0.8607 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: E 5 MET cc_start: 0.2141 (ptm) cc_final: 0.1406 (ptm) REVERT: E 100 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3670 (mm) REVERT: E 253 MET cc_start: 0.1777 (tpt) cc_final: 0.1540 (tpt) REVERT: E 276 MET cc_start: 0.7793 (ppp) cc_final: 0.6885 (ppp) REVERT: E 280 MET cc_start: 0.8727 (mtm) cc_final: 0.8473 (mtm) outliers start: 25 outliers final: 19 residues processed: 92 average time/residue: 0.2079 time to fit residues: 28.1242 Evaluate side-chains 87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 261 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 71 THR Chi-restraints excluded: chain D residue 19 CYS 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 163 ASN Chi-restraints excluded: chain E residue 299 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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** C 10 ASN C 110 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9508 Z= 0.165 Angle : 0.594 11.665 12863 Z= 0.301 Chirality : 0.044 0.210 1508 Planarity : 0.003 0.047 1651 Dihedral : 4.346 20.510 1301 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 20.78 % Favored : 77.48 % 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: 0.39 (0.25), residues: 1197 helix: 1.46 (0.21), residues: 602 sheet: -1.39 (0.40), residues: 166 loop : -0.70 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 205 HIS 0.006 0.001 HIS F 63 PHE 0.013 0.001 PHE A 242 TYR 0.017 0.001 TYR C 103 ARG 0.003 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 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7611 (pmm) cc_final: 0.6921 (pmm) REVERT: C 17 PHE cc_start: 0.8694 (m-80) cc_final: 0.8031 (m-80) REVERT: C 116 MET cc_start: 0.7136 (mmm) cc_final: 0.5880 (mpp) REVERT: D 46 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8339 (Cg_endo) REVERT: F 17 PHE cc_start: 0.7802 (m-80) cc_final: 0.7483 (m-80) REVERT: E 5 MET cc_start: 0.2050 (ptm) cc_final: 0.1330 (ptm) REVERT: E 100 LEU cc_start: 0.4026 (OUTLIER) cc_final: 0.3553 (mm) REVERT: E 253 MET cc_start: 0.1737 (tpt) cc_final: 0.1514 (tpt) REVERT: E 276 MET cc_start: 0.7766 (ppp) cc_final: 0.6839 (ppp) REVERT: E 280 MET cc_start: 0.8659 (mtm) cc_final: 0.8417 (mtm) REVERT: E 299 ASN cc_start: 0.4039 (OUTLIER) cc_final: 0.3019 (t0) REVERT: E 302 MET cc_start: 0.4301 (tpp) cc_final: 0.3340 (tpp) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1968 time to fit residues: 26.7788 Evaluate side-chains 90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 261 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 71 THR Chi-restraints excluded: chain D residue 19 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4211 r_free = 0.4211 target = 0.086336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.070126 restraints weight = 54318.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.071876 restraints weight = 32685.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.073034 restraints weight = 23071.843| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2634 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= 0.206 Angle : 0.609 10.177 12863 Z= 0.313 Chirality : 0.044 0.182 1508 Planarity : 0.003 0.043 1651 Dihedral : 4.395 20.539 1301 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.75 % Allowed : 20.97 % Favored : 77.28 % 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: 0.29 (0.25), residues: 1197 helix: 1.34 (0.21), residues: 606 sheet: -1.32 (0.40), residues: 166 loop : -0.76 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.005 0.001 HIS F 63 PHE 0.010 0.001 PHE E 10 TYR 0.015 0.002 TYR F 35 ARG 0.004 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.46 seconds wall clock time: 41 minutes 50.59 seconds (2510.59 seconds total)