Starting phenix.real_space_refine on Thu Jul 2 16:54:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tzo_41764/07_2026/8tzo_41764.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.077 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 73 5.16 5 C 5627 2.51 5 N 1450 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8737 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2341 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "C" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2218 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8737 At special positions: 0 Unit cell: (106.24, 118.69, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 73 16.00 P 1 15.00 O 1585 8.00 N 1450 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 131 " distance=2.02 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 137 " 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=1, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 295 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 352.8 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 42.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 55 through 77 removed outlier: 4.407A pdb=" N ILE A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 125 removed outlier: 3.571A pdb=" N GLN A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.752A pdb=" N TYR A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.533A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.566A pdb=" N CYS A 308 " --> pdb=" O CYS A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.649A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.563A pdb=" N ILE B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 322 Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 361 Proline residue: B 341 - end of helix removed outlier: 4.589A pdb=" N VAL B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 412 removed outlier: 4.251A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 removed outlier: 4.025A pdb=" N PHE B 474 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.788A pdb=" N SER C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.827A pdb=" N MET C 122 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.861A pdb=" N ILE C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 377 removed outlier: 5.147A pdb=" N VAL C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 254 removed outlier: 4.640A pdb=" N PHE A 251 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 removed outlier: 3.956A pdb=" N TYR A 346 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.963A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.538A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.503A pdb=" N PHE C 330 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 325 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.503A pdb=" N PHE C 330 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE C 327 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS C 98 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN C 329 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR C 96 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR C 182 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C 193 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 184 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.314A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.314A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1287 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: 1.37 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2525 1.44 - 1.56: 4924 1.56 - 1.69: 3 1.69 - 1.82: 107 Bond restraints: 8959 Sorted by residual: bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.16e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.435 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" N POV B 601 " pdb=" C12 POV B 601 " ideal model delta sigma weight residual 1.508 1.455 0.053 2.00e-02 2.50e+03 6.95e+00 ... (remaining 8954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11916 2.49 - 4.99: 153 4.99 - 7.48: 17 7.48 - 9.97: 7 9.97 - 12.47: 2 Bond angle restraints: 12095 Sorted by residual: angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 110.14 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.16 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C22 POV B 601 " pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 111.03 120.33 -9.30 3.00e+00 1.11e-01 9.61e+00 angle pdb=" C32 POV B 601 " pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 110.66 119.95 -9.29 3.00e+00 1.11e-01 9.60e+00 angle pdb=" N POV B 601 " pdb=" C12 POV B 601 " pdb=" C11 POV B 601 " ideal model delta sigma weight residual 118.03 108.89 9.14 3.00e+00 1.11e-01 9.28e+00 ... (remaining 12090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4753 17.91 - 35.82: 399 35.82 - 53.73: 98 53.73 - 71.64: 20 71.64 - 89.55: 16 Dihedral angle restraints: 5286 sinusoidal: 2202 harmonic: 3084 Sorted by residual: dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA CYS A 331 " pdb=" C CYS A 331 " pdb=" N CYS A 332 " pdb=" CA CYS A 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PHE A 328 " pdb=" C PHE A 328 " pdb=" N HIS A 329 " pdb=" CA HIS A 329 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1091 0.057 - 0.114: 189 0.114 - 0.171: 17 0.171 - 0.227: 2 0.227 - 0.284: 1 Chirality restraints: 1300 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2 MAN D 4 " pdb=" C1 MAN D 4 " pdb=" C3 MAN D 4 " pdb=" O2 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.52 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1297 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 177 " -0.057 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO C 178 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 281 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 282 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 298 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 299 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.028 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1883 2.78 - 3.31: 8331 3.31 - 3.84: 14574 3.84 - 4.37: 17165 4.37 - 4.90: 29956 Nonbonded interactions: 71909 Sorted by model distance: nonbonded pdb=" O LYS A 173 " pdb=" OG1 THR A 178 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU B 285 " pdb=" NH2 ARG B 303 " model vdw 2.256 3.120 nonbonded pdb=" NE2 HIS A 329 " pdb=" OE2 GLU B 205 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR C 128 " pdb=" O3 GLC D 7 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 342 " pdb=" OD2 ASP C 201 " model vdw 2.359 3.120 ... (remaining 71904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.410 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.004 0.091 8982 Z= 0.200 Angle : 0.711 12.465 12146 Z= 0.355 Chirality : 0.042 0.284 1300 Planarity : 0.005 0.087 1525 Dihedral : 15.086 89.553 3259 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.22 % Allowed : 8.93 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.26), residues: 1060 helix: 2.15 (0.25), residues: 399 sheet: -0.52 (0.37), residues: 206 loop : -0.33 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.020 0.001 TYR C 338 PHE 0.015 0.001 PHE C 342 TRP 0.018 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 8959) covalent geometry : angle 0.70111 / 0.35 (12095) SS BOND : bond 0.00270 / 0.15 ( 15) SS BOND : angle 1.04407 / 0.69 ( 30) hydrogen bonds : bond 0.15403 / 10.02 ( 437) hydrogen bonds : angle 6.87683 / 5.16 ( 1287) Misc. bond : bond 0.00023 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00357 / 0.19 ( 2) link_ALPHA1-2 : angle 3.36655 / 1.89 ( 6) link_ALPHA1-3 : bond 0.00567 / 0.28 ( 2) link_ALPHA1-3 : angle 1.49758 / 0.82 ( 6) link_BETA1-4 : bond 0.00547 / 0.27 ( 2) link_BETA1-4 : angle 2.80386 / 1.40 ( 6) link_NAG-ASN : bond 0.00377 / 0.20 ( 1) link_NAG-ASN : angle 3.53799 / 1.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: B 254 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7965 (mtp85) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.0741 time to fit residues: 10.9091 Evaluate side-chains 94 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0010 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.195194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122896 restraints weight = 9852.429| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.43 r_work: 0.3317 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8982 Z= 0.115 Angle : 0.536 6.981 12146 Z= 0.280 Chirality : 0.041 0.206 1300 Planarity : 0.005 0.065 1525 Dihedral : 7.898 85.602 1195 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 8.18 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.26), residues: 1060 helix: 2.54 (0.25), residues: 386 sheet: -0.16 (0.38), residues: 198 loop : -0.29 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.016 0.001 TYR A 318 PHE 0.016 0.001 PHE C 113 TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8959) covalent geometry : angle 0.52738 / 0.28 (12095) SS BOND : bond 0.00305 / 0.21 ( 15) SS BOND : angle 0.89312 / 0.57 ( 30) hydrogen bonds : bond 0.04511 / 2.98 ( 437) hydrogen bonds : angle 4.90975 / 3.66 ( 1287) Misc. bond : bond 0.00028 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00433 / 0.22 ( 2) link_ALPHA1-2 : angle 2.78145 / 1.58 ( 6) link_ALPHA1-3 : bond 0.00796 / 0.40 ( 2) link_ALPHA1-3 : angle 1.39718 / 0.80 ( 6) link_BETA1-4 : bond 0.00173 / 0.09 ( 2) link_BETA1-4 : angle 1.52886 / 0.66 ( 6) link_NAG-ASN : bond 0.00298 / 0.16 ( 1) link_NAG-ASN : angle 3.14891 / 1.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.319 Fit side-chains REVERT: C 168 PHE cc_start: 0.5302 (t80) cc_final: 0.4946 (t80) REVERT: C 169 THR cc_start: 0.6928 (m) cc_final: 0.6537 (p) REVERT: C 357 MET cc_start: 0.6275 (tpp) cc_final: 0.6028 (tpt) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.0805 time to fit residues: 13.7728 Evaluate side-chains 106 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 195 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.191099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118105 restraints weight = 9912.309| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.43 r_work: 0.3244 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8982 Z= 0.222 Angle : 0.598 7.935 12146 Z= 0.308 Chirality : 0.044 0.194 1300 Planarity : 0.005 0.055 1525 Dihedral : 7.407 85.591 1193 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.26 % Allowed : 9.69 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1060 helix: 2.28 (0.24), residues: 388 sheet: -0.41 (0.38), residues: 196 loop : -0.39 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.017 0.002 TYR A 318 PHE 0.020 0.002 PHE C 113 TRP 0.015 0.002 TRP A 147 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 ( 8959) covalent geometry : angle 0.59086 / 0.31 (12095) SS BOND : bond 0.00558 / 0.32 ( 15) SS BOND : angle 1.02871 / 0.63 ( 30) hydrogen bonds : bond 0.04843 / 3.30 ( 437) hydrogen bonds : angle 4.77144 / 3.54 ( 1287) Misc. bond : bond 0.00038 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00136 / 0.07 ( 2) link_ALPHA1-2 : angle 2.68210 / 1.53 ( 6) link_ALPHA1-3 : bond 0.00409 / 0.20 ( 2) link_ALPHA1-3 : angle 1.46821 / 0.84 ( 6) link_BETA1-4 : bond 0.00014 / 0.01 ( 2) link_BETA1-4 : angle 1.43665 / 0.66 ( 6) link_NAG-ASN : bond 0.00283 / 0.15 ( 1) link_NAG-ASN : angle 2.93111 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.337 Fit side-chains REVERT: C 120 THR cc_start: 0.8284 (p) cc_final: 0.7970 (t) REVERT: C 168 PHE cc_start: 0.5623 (t80) cc_final: 0.5128 (t80) REVERT: C 318 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7200 (pp) REVERT: C 357 MET cc_start: 0.6363 (tpp) cc_final: 0.6031 (tpt) outliers start: 21 outliers final: 15 residues processed: 118 average time/residue: 0.0699 time to fit residues: 12.2345 Evaluate side-chains 113 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 459 HIS C 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.193540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123009 restraints weight = 10025.214| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.98 r_work: 0.3260 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8982 Z= 0.142 Angle : 0.538 7.086 12146 Z= 0.280 Chirality : 0.041 0.187 1300 Planarity : 0.004 0.049 1525 Dihedral : 7.118 83.070 1193 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.37 % Allowed : 11.19 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1060 helix: 2.55 (0.25), residues: 382 sheet: -0.47 (0.38), residues: 197 loop : -0.32 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.014 0.001 TYR A 318 PHE 0.016 0.001 PHE C 113 TRP 0.014 0.001 TRP B 481 HIS 0.007 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8959) covalent geometry : angle 0.53077 / 0.28 (12095) SS BOND : bond 0.00323 / 0.20 ( 15) SS BOND : angle 0.87523 / 0.55 ( 30) hydrogen bonds : bond 0.04211 / 2.84 ( 437) hydrogen bonds : angle 4.51971 / 3.36 ( 1287) Misc. bond : bond 0.00034 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00292 / 0.15 ( 2) link_ALPHA1-2 : angle 2.47881 / 1.41 ( 6) link_ALPHA1-3 : bond 0.00608 / 0.30 ( 2) link_ALPHA1-3 : angle 1.33124 / 0.76 ( 6) link_BETA1-4 : bond 0.00116 / 0.06 ( 2) link_BETA1-4 : angle 1.29815 / 0.60 ( 6) link_NAG-ASN : bond 0.00277 / 0.15 ( 1) link_NAG-ASN : angle 2.80192 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 79 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 258 MET cc_start: 0.8056 (mtp) cc_final: 0.7777 (mtp) REVERT: B 285 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 323 MET cc_start: 0.8454 (mmm) cc_final: 0.8191 (mmm) REVERT: B 461 LYS cc_start: 0.8082 (tptp) cc_final: 0.7850 (tptp) REVERT: C 168 PHE cc_start: 0.5535 (t80) cc_final: 0.5215 (t80) REVERT: C 318 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7211 (pp) REVERT: C 357 MET cc_start: 0.6320 (tpp) cc_final: 0.6014 (tpp) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.0665 time to fit residues: 11.5304 Evaluate side-chains 117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 459 HIS C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119231 restraints weight = 9866.425| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.41 r_work: 0.3275 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8982 Z= 0.162 Angle : 0.544 7.371 12146 Z= 0.281 Chirality : 0.042 0.174 1300 Planarity : 0.004 0.046 1525 Dihedral : 6.919 78.247 1193 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.37 % Allowed : 11.73 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1060 helix: 2.51 (0.25), residues: 385 sheet: -0.52 (0.38), residues: 194 loop : -0.41 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.013 0.001 TYR C 150 PHE 0.017 0.001 PHE C 113 TRP 0.014 0.001 TRP A 147 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 8959) covalent geometry : angle 0.53735 / 0.28 (12095) SS BOND : bond 0.00381 / 0.23 ( 15) SS BOND : angle 0.82861 / 0.51 ( 30) hydrogen bonds : bond 0.04231 / 2.87 ( 437) hydrogen bonds : angle 4.44949 / 3.31 ( 1287) Misc. bond : bond 0.00027 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00251 / 0.12 ( 2) link_ALPHA1-2 : angle 2.45066 / 1.39 ( 6) link_ALPHA1-3 : bond 0.00479 / 0.23 ( 2) link_ALPHA1-3 : angle 1.38342 / 0.79 ( 6) link_BETA1-4 : bond 0.00131 / 0.07 ( 2) link_BETA1-4 : angle 1.24961 / 0.58 ( 6) link_NAG-ASN : bond 0.00296 / 0.16 ( 1) link_NAG-ASN : angle 2.82244 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.304 Fit side-chains REVERT: B 79 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 254 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7872 (mtp85) REVERT: B 285 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: B 323 MET cc_start: 0.8443 (mmm) cc_final: 0.8138 (mmm) REVERT: B 405 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7227 (ttp-170) REVERT: B 461 LYS cc_start: 0.8128 (tptp) cc_final: 0.7871 (tptp) REVERT: C 98 LYS cc_start: 0.7075 (ptmt) cc_final: 0.6775 (ptmt) REVERT: C 120 THR cc_start: 0.8317 (p) cc_final: 0.8028 (t) REVERT: C 318 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7212 (pp) REVERT: C 357 MET cc_start: 0.6421 (tpp) cc_final: 0.6098 (tpp) outliers start: 22 outliers final: 16 residues processed: 123 average time/residue: 0.0839 time to fit residues: 14.7434 Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.192614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120415 restraints weight = 9867.956| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.42 r_work: 0.3291 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8982 Z= 0.137 Angle : 0.528 7.043 12146 Z= 0.274 Chirality : 0.041 0.181 1300 Planarity : 0.004 0.045 1525 Dihedral : 6.759 73.317 1193 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.94 % Allowed : 12.27 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1060 helix: 2.57 (0.24), residues: 387 sheet: -0.49 (0.38), residues: 193 loop : -0.37 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.015 0.001 TYR C 150 PHE 0.016 0.001 PHE C 113 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8959) covalent geometry : angle 0.52076 / 0.27 (12095) SS BOND : bond 0.00302 / 0.19 ( 15) SS BOND : angle 0.97011 / 0.59 ( 30) hydrogen bonds : bond 0.04031 / 2.72 ( 437) hydrogen bonds : angle 4.36517 / 3.24 ( 1287) Misc. bond : bond 0.00021 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00305 / 0.15 ( 2) link_ALPHA1-2 : angle 2.36895 / 1.34 ( 6) link_ALPHA1-3 : bond 0.00506 / 0.25 ( 2) link_ALPHA1-3 : angle 1.35837 / 0.77 ( 6) link_BETA1-4 : bond 0.00150 / 0.08 ( 2) link_BETA1-4 : angle 1.21243 / 0.56 ( 6) link_NAG-ASN : bond 0.00298 / 0.16 ( 1) link_NAG-ASN : angle 2.79537 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.329 Fit side-chains REVERT: B 79 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 258 MET cc_start: 0.8132 (mtp) cc_final: 0.7788 (mtp) REVERT: B 285 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: B 323 MET cc_start: 0.8455 (mmm) cc_final: 0.8141 (mmm) REVERT: B 405 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7264 (ttp80) REVERT: B 461 LYS cc_start: 0.8146 (tptp) cc_final: 0.7877 (tptp) REVERT: C 98 LYS cc_start: 0.7122 (ptmt) cc_final: 0.6869 (ptmt) REVERT: C 120 THR cc_start: 0.8366 (p) cc_final: 0.8093 (t) REVERT: C 318 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7216 (pp) REVERT: C 357 MET cc_start: 0.6449 (tpp) cc_final: 0.6215 (tpp) outliers start: 18 outliers final: 15 residues processed: 120 average time/residue: 0.0867 time to fit residues: 15.0107 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.191755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119242 restraints weight = 10012.777| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.46 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8982 Z= 0.159 Angle : 0.537 7.270 12146 Z= 0.277 Chirality : 0.041 0.182 1300 Planarity : 0.004 0.043 1525 Dihedral : 6.692 70.059 1193 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.05 % Allowed : 12.27 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1060 helix: 2.57 (0.24), residues: 385 sheet: -0.57 (0.38), residues: 192 loop : -0.42 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.013 0.001 TYR C 150 PHE 0.017 0.001 PHE C 113 TRP 0.014 0.001 TRP A 147 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 8959) covalent geometry : angle 0.53000 / 0.28 (12095) SS BOND : bond 0.00313 / 0.19 ( 15) SS BOND : angle 0.93310 / 0.57 ( 30) hydrogen bonds : bond 0.04146 / 2.82 ( 437) hydrogen bonds : angle 4.36093 / 3.24 ( 1287) Misc. bond : bond 0.00022 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00261 / 0.13 ( 2) link_ALPHA1-2 : angle 2.38084 / 1.35 ( 6) link_ALPHA1-3 : bond 0.00493 / 0.24 ( 2) link_ALPHA1-3 : angle 1.41509 / 0.80 ( 6) link_BETA1-4 : bond 0.00154 / 0.08 ( 2) link_BETA1-4 : angle 1.21719 / 0.57 ( 6) link_NAG-ASN : bond 0.00282 / 0.15 ( 1) link_NAG-ASN : angle 2.72890 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.234 Fit side-chains REVERT: A 181 ASN cc_start: 0.8913 (m-40) cc_final: 0.8522 (m-40) REVERT: B 76 ASP cc_start: 0.7802 (p0) cc_final: 0.7522 (p0) REVERT: B 254 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7872 (mtp85) REVERT: B 258 MET cc_start: 0.8134 (mtp) cc_final: 0.7623 (mtp) REVERT: B 285 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: B 323 MET cc_start: 0.8436 (mmm) cc_final: 0.8097 (mmm) REVERT: B 405 ARG cc_start: 0.7671 (tpt170) cc_final: 0.7248 (ttp80) REVERT: C 98 LYS cc_start: 0.7149 (ptmt) cc_final: 0.6816 (ptmt) REVERT: C 120 THR cc_start: 0.8355 (p) cc_final: 0.8109 (t) REVERT: C 318 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7244 (pp) REVERT: C 357 MET cc_start: 0.6353 (tpp) cc_final: 0.6124 (tpp) outliers start: 19 outliers final: 15 residues processed: 122 average time/residue: 0.0735 time to fit residues: 13.1098 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.193036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121107 restraints weight = 9876.585| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.41 r_work: 0.3297 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8982 Z= 0.126 Angle : 0.517 6.948 12146 Z= 0.268 Chirality : 0.041 0.178 1300 Planarity : 0.004 0.042 1525 Dihedral : 6.585 68.856 1193 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 12.70 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1060 helix: 2.65 (0.24), residues: 387 sheet: -0.42 (0.39), residues: 188 loop : -0.44 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.015 0.001 TYR C 150 PHE 0.015 0.001 PHE C 113 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8959) covalent geometry : angle 0.50998 / 0.27 (12095) SS BOND : bond 0.00291 / 0.18 ( 15) SS BOND : angle 0.88429 / 0.55 ( 30) hydrogen bonds : bond 0.03926 / 2.65 ( 437) hydrogen bonds : angle 4.26695 / 3.16 ( 1287) Misc. bond : bond 0.00012 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00324 / 0.16 ( 2) link_ALPHA1-2 : angle 2.33085 / 1.31 ( 6) link_ALPHA1-3 : bond 0.00497 / 0.24 ( 2) link_ALPHA1-3 : angle 1.42775 / 0.81 ( 6) link_BETA1-4 : bond 0.00150 / 0.08 ( 2) link_BETA1-4 : angle 1.15087 / 0.54 ( 6) link_NAG-ASN : bond 0.00265 / 0.14 ( 1) link_NAG-ASN : angle 2.67503 / 1.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.256 Fit side-chains REVERT: A 181 ASN cc_start: 0.8897 (m-40) cc_final: 0.8509 (m-40) REVERT: B 254 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7794 (mtp85) REVERT: B 258 MET cc_start: 0.8106 (mtp) cc_final: 0.7530 (mtp) REVERT: B 285 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: B 323 MET cc_start: 0.8418 (mmm) cc_final: 0.8094 (mmm) REVERT: B 405 ARG cc_start: 0.7692 (tpt170) cc_final: 0.7251 (ttp80) REVERT: C 98 LYS cc_start: 0.7175 (ptmt) cc_final: 0.6848 (ptmt) REVERT: C 120 THR cc_start: 0.8381 (p) cc_final: 0.8146 (t) REVERT: C 318 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7219 (pp) REVERT: C 357 MET cc_start: 0.6376 (tpp) cc_final: 0.6137 (tpp) outliers start: 18 outliers final: 15 residues processed: 119 average time/residue: 0.0786 time to fit residues: 13.6322 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121701 restraints weight = 9910.312| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.46 r_work: 0.3306 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8982 Z= 0.121 Angle : 0.512 6.905 12146 Z= 0.264 Chirality : 0.041 0.174 1300 Planarity : 0.004 0.041 1525 Dihedral : 6.442 67.262 1193 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.83 % Allowed : 12.81 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1060 helix: 2.69 (0.24), residues: 387 sheet: -0.40 (0.39), residues: 188 loop : -0.41 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.015 0.001 TYR C 150 PHE 0.015 0.001 PHE C 113 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8959) covalent geometry : angle 0.50538 / 0.26 (12095) SS BOND : bond 0.00289 / 0.18 ( 15) SS BOND : angle 0.83261 / 0.53 ( 30) hydrogen bonds : bond 0.03826 / 2.59 ( 437) hydrogen bonds : angle 4.19808 / 3.11 ( 1287) Misc. bond : bond 0.00005 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00345 / 0.17 ( 2) link_ALPHA1-2 : angle 2.27026 / 1.27 ( 6) link_ALPHA1-3 : bond 0.00505 / 0.24 ( 2) link_ALPHA1-3 : angle 1.44509 / 0.81 ( 6) link_BETA1-4 : bond 0.00186 / 0.09 ( 2) link_BETA1-4 : angle 1.10460 / 0.52 ( 6) link_NAG-ASN : bond 0.00265 / 0.14 ( 1) link_NAG-ASN : angle 2.57409 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.334 Fit side-chains REVERT: A 181 ASN cc_start: 0.8891 (m-40) cc_final: 0.8502 (m-40) REVERT: B 254 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7831 (mtp85) REVERT: B 258 MET cc_start: 0.8121 (mtp) cc_final: 0.7555 (mtp) REVERT: B 285 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: B 323 MET cc_start: 0.8420 (mmm) cc_final: 0.8127 (mmm) REVERT: B 405 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7247 (ttp80) REVERT: C 98 LYS cc_start: 0.7221 (ptmt) cc_final: 0.6870 (ptmt) REVERT: C 120 THR cc_start: 0.8350 (p) cc_final: 0.8101 (t) REVERT: C 318 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7235 (pp) REVERT: C 357 MET cc_start: 0.6332 (tpp) cc_final: 0.6099 (tpp) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.0734 time to fit residues: 12.9920 Evaluate side-chains 114 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 322 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.194931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123346 restraints weight = 9904.539| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.42 r_work: 0.3327 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8982 Z= 0.107 Angle : 0.498 6.931 12146 Z= 0.257 Chirality : 0.040 0.170 1300 Planarity : 0.004 0.041 1525 Dihedral : 6.279 65.358 1193 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.72 % Allowed : 13.02 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1060 helix: 2.83 (0.25), residues: 387 sheet: -0.37 (0.39), residues: 188 loop : -0.41 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.024 0.001 TYR C 338 PHE 0.015 0.001 PHE C 113 TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8959) covalent geometry : angle 0.49099 / 0.26 (12095) SS BOND : bond 0.00316 / 0.18 ( 15) SS BOND : angle 0.97155 / 0.60 ( 30) hydrogen bonds : bond 0.03628 / 2.44 ( 437) hydrogen bonds : angle 4.10820 / 3.05 ( 1287) Misc. bond : bond 0.00009 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00393 / 0.20 ( 2) link_ALPHA1-2 : angle 2.19584 / 1.22 ( 6) link_ALPHA1-3 : bond 0.00526 / 0.26 ( 2) link_ALPHA1-3 : angle 1.45674 / 0.81 ( 6) link_BETA1-4 : bond 0.00173 / 0.09 ( 2) link_BETA1-4 : angle 1.10439 / 0.52 ( 6) link_NAG-ASN : bond 0.00251 / 0.13 ( 1) link_NAG-ASN : angle 2.50662 / 1.30 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.334 Fit side-chains REVERT: A 181 ASN cc_start: 0.8880 (m-40) cc_final: 0.8504 (m-40) REVERT: B 254 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7857 (mtp85) REVERT: B 258 MET cc_start: 0.8064 (mtp) cc_final: 0.7536 (mtp) REVERT: B 285 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: B 323 MET cc_start: 0.8429 (mmm) cc_final: 0.8178 (mmm) REVERT: B 405 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7237 (ttp80) REVERT: C 21 VAL cc_start: 0.7695 (t) cc_final: 0.7291 (p) REVERT: C 98 LYS cc_start: 0.7239 (ptmt) cc_final: 0.6885 (ptmt) REVERT: C 120 THR cc_start: 0.8370 (p) cc_final: 0.8117 (t) REVERT: C 318 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7226 (pp) REVERT: C 357 MET cc_start: 0.6328 (tpp) cc_final: 0.6102 (tpp) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.0805 time to fit residues: 13.9062 Evaluate side-chains 116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 322 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.193504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121421 restraints weight = 9835.465| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.40 r_work: 0.3301 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8982 Z= 0.139 Angle : 0.520 7.062 12146 Z= 0.268 Chirality : 0.041 0.172 1300 Planarity : 0.004 0.041 1525 Dihedral : 6.311 65.484 1193 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.61 % Allowed : 13.24 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1060 helix: 2.70 (0.24), residues: 387 sheet: -0.42 (0.39), residues: 185 loop : -0.44 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.014 0.001 TYR C 150 PHE 0.016 0.001 PHE C 113 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8959) covalent geometry : angle 0.51379 / 0.27 (12095) SS BOND : bond 0.00302 / 0.18 ( 15) SS BOND : angle 0.96888 / 0.59 ( 30) hydrogen bonds : bond 0.03885 / 2.64 ( 437) hydrogen bonds : angle 4.17092 / 3.09 ( 1287) Misc. bond : bond 0.00008 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00328 / 0.16 ( 2) link_ALPHA1-2 : angle 2.25063 / 1.26 ( 6) link_ALPHA1-3 : bond 0.00470 / 0.23 ( 2) link_ALPHA1-3 : angle 1.48134 / 0.83 ( 6) link_BETA1-4 : bond 0.00153 / 0.08 ( 2) link_BETA1-4 : angle 1.12606 / 0.53 ( 6) link_NAG-ASN : bond 0.00246 / 0.13 ( 1) link_NAG-ASN : angle 2.44929 / 1.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.86 seconds wall clock time: 46 minutes 38.57 seconds (2798.57 seconds total)