Starting phenix.real_space_refine on Fri Jun 6 06:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.map" model { file = "/net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qey_18379/06_2025/8qey_18379.cif" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4754 2.51 5 N 1185 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3462 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain: "B" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.17, per 1000 atoms: 0.71 Number of scatterers: 7306 At special positions: 0 Unit cell: (94.734, 83.931, 131.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1336 8.00 N 1185 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 109 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 601 " - " ASN B 264 " " NAG C 1 " - " ASN B 323 " " NAG D 1 " - " ASN B 280 " " NAG E 1 " - " ASN B 405 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 868.8 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 58.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.616A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.019A pdb=" N ILE A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.638A pdb=" N GLY A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.332A pdb=" N VAL A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.434A pdb=" N ALA A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.570A pdb=" N SER A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 4.048A pdb=" N PHE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.713A pdb=" N GLN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.652A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.670A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.817A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.868A pdb=" N LEU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 348 Proline residue: A 319 - end of helix removed outlier: 3.535A pdb=" N GLU A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.637A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 413 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 445 through 458 removed outlier: 3.806A pdb=" N CYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 4.156A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 487 removed outlier: 4.287A pdb=" N TRP A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 74 through 105 Processing helix chain 'B' and resid 128 through 134 Processing helix chain 'B' and resid 139 through 145 removed outlier: 4.105A pdb=" N LYS B 144 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.169A pdb=" N VAL B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 348 through 357 removed outlier: 4.472A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.565A pdb=" N ASP B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.598A pdb=" N SER B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 432 " --> pdb=" O GLN B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125 removed outlier: 6.662A pdb=" N TRP B 332 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N SER B 366 " --> pdb=" O TRP B 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165 removed outlier: 4.218A pdb=" N LYS B 165 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 175 " --> pdb=" O LYS B 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 206 removed outlier: 7.050A pdb=" N LEU B 205 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE B 244 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY B 278 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 246 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA B 277 " --> pdb=" O THR B 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.593A pdb=" N HIS B 441 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 524 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 494 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 492 " --> pdb=" O LEU B 508 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1068 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: 1.78 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1339 1.33 - 1.45: 1942 1.45 - 1.57: 4168 1.57 - 1.69: 2 1.69 - 1.82: 49 Bond restraints: 7500 Sorted by residual: bond pdb=" CB PRO B 526 " pdb=" CG PRO B 526 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.35e+00 bond pdb=" C65 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.373 1.407 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.75e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 7495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 10103 3.64 - 7.28: 105 7.28 - 10.92: 16 10.92 - 14.56: 3 14.56 - 18.20: 1 Bond angle restraints: 10228 Sorted by residual: angle pdb=" CA PRO B 526 " pdb=" N PRO B 526 " pdb=" CD PRO B 526 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" CA PRO A 149 " pdb=" N PRO A 149 " pdb=" CD PRO A 149 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 134.50 -18.20 3.50e+00 8.16e-02 2.70e+01 angle pdb=" C ILE A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 122.58 113.49 9.09 2.07e+00 2.33e-01 1.93e+01 angle pdb=" CA TYR A 337 " pdb=" CB TYR A 337 " pdb=" CG TYR A 337 " ideal model delta sigma weight residual 113.90 120.98 -7.08 1.80e+00 3.09e-01 1.55e+01 ... (remaining 10223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 4035 22.22 - 44.43: 472 44.43 - 66.65: 89 66.65 - 88.86: 28 88.86 - 111.08: 12 Dihedral angle restraints: 4636 sinusoidal: 2021 harmonic: 2615 Sorted by residual: dihedral pdb=" CA LEU A 350 " pdb=" C LEU A 350 " pdb=" N PRO A 351 " pdb=" CA PRO A 351 " ideal model delta harmonic sigma weight residual -180.00 -142.44 -37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual -86.00 -149.89 63.89 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA ILE A 100 " pdb=" C ILE A 100 " pdb=" N PRO A 101 " pdb=" CA PRO A 101 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1018 0.065 - 0.130: 166 0.130 - 0.196: 22 0.196 - 0.261: 5 0.261 - 0.326: 2 Chirality restraints: 1213 Sorted by residual: chirality pdb=" CG LEU B 233 " pdb=" CB LEU B 233 " pdb=" CD1 LEU B 233 " pdb=" CD2 LEU B 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 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 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C08 AJP A 601 " pdb=" C07 AJP A 601 " pdb=" C10 AJP A 601 " pdb=" O09 AJP A 601 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1210 not shown) Planarity restraints: 1254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 525 " 0.104 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO B 526 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " 0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 149 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " 0.020 2.00e-02 2.50e+03 2.08e-02 8.68e+00 pdb=" CG TYR A 399 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " 0.001 2.00e-02 2.50e+03 ... (remaining 1251 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1790 2.79 - 3.31: 7031 3.31 - 3.84: 12106 3.84 - 4.37: 12654 4.37 - 4.90: 21712 Nonbonded interactions: 55293 Sorted by model distance: nonbonded pdb=" OH TYR B 367 " pdb=" O PRO B 386 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR B 149 " pdb=" OE2 GLU B 370 " model vdw 2.289 3.040 nonbonded pdb=" O LYS B 315 " pdb=" OG1 THR B 319 " model vdw 2.289 3.040 nonbonded pdb=" O GLY A 57 " pdb=" OG SER A 61 " model vdw 2.289 3.040 nonbonded pdb=" O VAL A 279 " pdb=" OG1 THR A 283 " model vdw 2.291 3.040 ... (remaining 55288 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 'C' selection = chain 'E' } 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: 1.610 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.005 0.116 7509 Z= 0.213 Angle : 0.966 18.202 10254 Z= 0.453 Chirality : 0.052 0.326 1213 Planarity : 0.007 0.150 1250 Dihedral : 19.802 111.079 2959 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.91 % Allowed : 41.20 % Favored : 57.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.09 (0.27), residues: 914 helix: 0.30 (0.23), residues: 483 sheet: -0.51 (0.67), residues: 59 loop : -2.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 316 HIS 0.008 0.001 HIS A 213 PHE 0.045 0.002 PHE A 440 TYR 0.052 0.002 TYR A 399 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 1.77583 ( 12) link_BETA1-4 : bond 0.00756 ( 4) link_BETA1-4 : angle 3.11305 ( 12) hydrogen bonds : bond 0.12707 ( 363) hydrogen bonds : angle 5.85767 ( 1068) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.90394 ( 2) covalent geometry : bond 0.00478 ( 7500) covalent geometry : angle 0.95933 (10228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7980 (tp30) cc_final: 0.7032 (tm-30) REVERT: A 140 MET cc_start: 0.8817 (ttm) cc_final: 0.8589 (ttp) REVERT: A 215 GLU cc_start: 0.7309 (mp0) cc_final: 0.6593 (pm20) REVERT: A 221 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (p0) outliers start: 7 outliers final: 2 residues processed: 162 average time/residue: 0.1449 time to fit residues: 34.1210 Evaluate side-chains 154 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.0470 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144556 restraints weight = 12929.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143882 restraints weight = 9774.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145284 restraints weight = 8841.182| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7509 Z= 0.130 Angle : 0.679 10.398 10254 Z= 0.320 Chirality : 0.041 0.203 1213 Planarity : 0.005 0.091 1250 Dihedral : 11.745 96.323 1371 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 5.35 % Allowed : 34.55 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.28), residues: 914 helix: 1.01 (0.24), residues: 480 sheet: -0.57 (0.64), residues: 55 loop : -1.78 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.003 0.001 HIS B 441 PHE 0.014 0.001 PHE A 393 TYR 0.036 0.002 TYR A 399 ARG 0.007 0.000 ARG A 470 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 1.60274 ( 12) link_BETA1-4 : bond 0.00642 ( 4) link_BETA1-4 : angle 3.11775 ( 12) hydrogen bonds : bond 0.04012 ( 363) hydrogen bonds : angle 4.67161 ( 1068) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.21591 ( 2) covalent geometry : bond 0.00293 ( 7500) covalent geometry : angle 0.66889 (10228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7226 (mmm) REVERT: A 215 GLU cc_start: 0.7360 (mp0) cc_final: 0.6784 (pm20) REVERT: A 356 MET cc_start: 0.6417 (mpp) cc_final: 0.6055 (mpp) REVERT: B 302 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9090 (t) outliers start: 41 outliers final: 25 residues processed: 187 average time/residue: 0.1390 time to fit residues: 38.1855 Evaluate side-chains 179 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143451 restraints weight = 13130.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142887 restraints weight = 10044.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144051 restraints weight = 10136.105| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7509 Z= 0.126 Angle : 0.674 10.855 10254 Z= 0.312 Chirality : 0.042 0.322 1213 Planarity : 0.004 0.071 1250 Dihedral : 10.412 87.053 1369 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 7.04 % Allowed : 33.90 % Favored : 59.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.02 (0.28), residues: 914 helix: 1.28 (0.24), residues: 485 sheet: -0.50 (0.65), residues: 56 loop : -1.65 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.003 0.001 HIS B 313 PHE 0.010 0.001 PHE B 525 TYR 0.031 0.002 TYR A 399 ARG 0.002 0.000 ARG B 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 1.59058 ( 12) link_BETA1-4 : bond 0.00642 ( 4) link_BETA1-4 : angle 3.25593 ( 12) hydrogen bonds : bond 0.03783 ( 363) hydrogen bonds : angle 4.42424 ( 1068) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.86250 ( 2) covalent geometry : bond 0.00281 ( 7500) covalent geometry : angle 0.66277 (10228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7407 (mp0) cc_final: 0.6894 (pm20) REVERT: A 221 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7279 (p0) REVERT: A 356 MET cc_start: 0.6632 (mpp) cc_final: 0.6265 (mpp) REVERT: A 360 ARG cc_start: 0.2263 (OUTLIER) cc_final: 0.1201 (ttp-170) REVERT: B 302 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.9011 (t) REVERT: B 336 GLN cc_start: 0.8636 (tp40) cc_final: 0.8238 (tp-100) outliers start: 54 outliers final: 32 residues processed: 204 average time/residue: 0.1782 time to fit residues: 53.3919 Evaluate side-chains 198 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140393 restraints weight = 13206.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141386 restraints weight = 9686.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143055 restraints weight = 8133.868| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7509 Z= 0.119 Angle : 0.671 8.392 10254 Z= 0.310 Chirality : 0.041 0.274 1213 Planarity : 0.004 0.061 1250 Dihedral : 9.603 77.465 1369 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.52 % Allowed : 36.25 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.18 (0.29), residues: 914 helix: 1.42 (0.24), residues: 486 sheet: -0.37 (0.66), residues: 56 loop : -1.61 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 316 HIS 0.002 0.000 HIS A 68 PHE 0.016 0.001 PHE A 463 TYR 0.025 0.002 TYR A 399 ARG 0.001 0.000 ARG B 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 4) link_NAG-ASN : angle 1.58097 ( 12) link_BETA1-4 : bond 0.00660 ( 4) link_BETA1-4 : angle 3.31287 ( 12) hydrogen bonds : bond 0.03623 ( 363) hydrogen bonds : angle 4.33217 ( 1068) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.89872 ( 2) covalent geometry : bond 0.00263 ( 7500) covalent geometry : angle 0.66011 (10228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7923 (tp30) cc_final: 0.6935 (tm-30) REVERT: A 166 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: A 215 GLU cc_start: 0.7383 (mp0) cc_final: 0.6920 (pm20) REVERT: A 221 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7343 (p0) REVERT: A 360 ARG cc_start: 0.2237 (OUTLIER) cc_final: 0.1245 (ttp-170) REVERT: B 237 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 302 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9000 (t) REVERT: B 336 GLN cc_start: 0.8638 (tp40) cc_final: 0.8174 (tp-100) outliers start: 50 outliers final: 32 residues processed: 200 average time/residue: 0.1891 time to fit residues: 55.2037 Evaluate side-chains 195 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.177561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140464 restraints weight = 13903.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141881 restraints weight = 9578.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143530 restraints weight = 7577.677| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7509 Z= 0.141 Angle : 0.694 11.685 10254 Z= 0.321 Chirality : 0.042 0.253 1213 Planarity : 0.004 0.056 1250 Dihedral : 9.073 68.835 1367 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 7.56 % Allowed : 35.07 % Favored : 57.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.36 (0.29), residues: 914 helix: 1.60 (0.24), residues: 480 sheet: -0.23 (0.68), residues: 56 loop : -1.54 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.002 0.001 HIS B 313 PHE 0.013 0.001 PHE A 433 TYR 0.015 0.001 TYR A 337 ARG 0.001 0.000 ARG A 470 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 1.61266 ( 12) link_BETA1-4 : bond 0.00712 ( 4) link_BETA1-4 : angle 3.39754 ( 12) hydrogen bonds : bond 0.03798 ( 363) hydrogen bonds : angle 4.36701 ( 1068) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.79102 ( 2) covalent geometry : bond 0.00322 ( 7500) covalent geometry : angle 0.68241 (10228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7952 (tp30) cc_final: 0.7003 (tm-30) REVERT: A 140 MET cc_start: 0.8761 (ttm) cc_final: 0.8518 (ttp) REVERT: A 215 GLU cc_start: 0.7395 (mp0) cc_final: 0.6917 (pm20) REVERT: A 221 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7231 (p0) REVERT: A 256 GLU cc_start: 0.8525 (tp30) cc_final: 0.8320 (tp30) REVERT: A 354 LEU cc_start: 0.8098 (tp) cc_final: 0.7866 (tp) REVERT: A 356 MET cc_start: 0.6442 (mpp) cc_final: 0.6002 (mpp) REVERT: A 360 ARG cc_start: 0.2056 (OUTLIER) cc_final: 0.1051 (ttp-170) REVERT: B 302 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.8953 (t) REVERT: B 336 GLN cc_start: 0.8622 (tp40) cc_final: 0.8068 (tp-100) REVERT: B 426 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8058 (t) outliers start: 58 outliers final: 38 residues processed: 201 average time/residue: 0.1406 time to fit residues: 41.4289 Evaluate side-chains 197 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136358 restraints weight = 13758.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140018 restraints weight = 8782.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142468 restraints weight = 6776.274| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7509 Z= 0.148 Angle : 0.693 10.170 10254 Z= 0.325 Chirality : 0.042 0.196 1213 Planarity : 0.004 0.053 1250 Dihedral : 8.389 57.398 1367 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 7.56 % Allowed : 34.29 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 914 helix: 1.54 (0.24), residues: 489 sheet: -0.20 (0.68), residues: 56 loop : -1.62 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 316 HIS 0.002 0.001 HIS B 119 PHE 0.013 0.001 PHE B 244 TYR 0.032 0.002 TYR A 399 ARG 0.003 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 1.60203 ( 12) link_BETA1-4 : bond 0.00820 ( 4) link_BETA1-4 : angle 3.38668 ( 12) hydrogen bonds : bond 0.03906 ( 363) hydrogen bonds : angle 4.35260 ( 1068) SS BOND : bond 0.00206 ( 1) SS BOND : angle 1.00777 ( 2) covalent geometry : bond 0.00341 ( 7500) covalent geometry : angle 0.68141 (10228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7230 (p0) REVERT: A 270 PHE cc_start: 0.5875 (m-80) cc_final: 0.5304 (m-80) REVERT: A 354 LEU cc_start: 0.8141 (tp) cc_final: 0.7899 (tp) REVERT: A 356 MET cc_start: 0.6534 (mpp) cc_final: 0.6147 (mpp) REVERT: A 360 ARG cc_start: 0.2036 (OUTLIER) cc_final: 0.1056 (ttp-170) REVERT: B 302 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9104 (t) REVERT: B 336 GLN cc_start: 0.8653 (tp40) cc_final: 0.8240 (tp40) REVERT: B 426 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8253 (t) outliers start: 58 outliers final: 42 residues processed: 204 average time/residue: 0.1507 time to fit residues: 44.7431 Evaluate side-chains 204 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 32 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139161 restraints weight = 13661.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142937 restraints weight = 8629.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145452 restraints weight = 6606.355| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7509 Z= 0.121 Angle : 0.703 9.911 10254 Z= 0.327 Chirality : 0.041 0.175 1213 Planarity : 0.004 0.052 1250 Dihedral : 7.954 57.727 1367 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.61 % Allowed : 35.46 % Favored : 58.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.48 (0.29), residues: 914 helix: 1.67 (0.24), residues: 485 sheet: -0.04 (0.69), residues: 56 loop : -1.50 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.013 0.001 HIS A 213 PHE 0.020 0.001 PHE A 463 TYR 0.031 0.002 TYR A 399 ARG 0.002 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.63950 ( 12) link_BETA1-4 : bond 0.00886 ( 4) link_BETA1-4 : angle 3.25848 ( 12) hydrogen bonds : bond 0.03679 ( 363) hydrogen bonds : angle 4.24312 ( 1068) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.97593 ( 2) covalent geometry : bond 0.00273 ( 7500) covalent geometry : angle 0.69262 (10228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8628 (t) REVERT: A 221 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7364 (p0) REVERT: A 253 TYR cc_start: 0.7650 (m-80) cc_final: 0.7152 (m-80) REVERT: A 270 PHE cc_start: 0.5810 (m-80) cc_final: 0.5230 (m-80) REVERT: A 354 LEU cc_start: 0.7972 (tp) cc_final: 0.7746 (tp) REVERT: A 356 MET cc_start: 0.6488 (mpp) cc_final: 0.6092 (mpp) REVERT: B 158 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8428 (tt) REVERT: B 426 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8154 (t) outliers start: 43 outliers final: 31 residues processed: 201 average time/residue: 0.1646 time to fit residues: 48.0604 Evaluate side-chains 197 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141953 restraints weight = 13758.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143902 restraints weight = 8938.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145219 restraints weight = 6697.266| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7509 Z= 0.136 Angle : 0.733 10.085 10254 Z= 0.340 Chirality : 0.044 0.211 1213 Planarity : 0.004 0.050 1250 Dihedral : 7.850 57.422 1367 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.74 % Allowed : 36.11 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.48 (0.29), residues: 914 helix: 1.67 (0.24), residues: 480 sheet: -0.08 (0.68), residues: 56 loop : -1.45 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 316 HIS 0.007 0.001 HIS B 313 PHE 0.027 0.001 PHE A 433 TYR 0.027 0.002 TYR A 399 ARG 0.001 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 4) link_NAG-ASN : angle 1.69348 ( 12) link_BETA1-4 : bond 0.00856 ( 4) link_BETA1-4 : angle 3.20185 ( 12) hydrogen bonds : bond 0.03817 ( 363) hydrogen bonds : angle 4.30042 ( 1068) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.06565 ( 2) covalent geometry : bond 0.00316 ( 7500) covalent geometry : angle 0.72285 (10228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7366 (p0) REVERT: A 354 LEU cc_start: 0.7975 (tp) cc_final: 0.7736 (tp) REVERT: A 356 MET cc_start: 0.6453 (mpp) cc_final: 0.6042 (mpp) REVERT: B 158 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8355 (tt) REVERT: B 426 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8143 (t) outliers start: 44 outliers final: 33 residues processed: 202 average time/residue: 0.1592 time to fit residues: 48.0971 Evaluate side-chains 198 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143535 restraints weight = 13931.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145583 restraints weight = 9360.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146492 restraints weight = 8258.896| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7509 Z= 0.125 Angle : 0.717 9.930 10254 Z= 0.334 Chirality : 0.043 0.202 1213 Planarity : 0.004 0.049 1250 Dihedral : 7.691 57.542 1367 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.95 % Allowed : 36.38 % Favored : 58.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.46 (0.29), residues: 914 helix: 1.66 (0.24), residues: 481 sheet: 0.01 (0.70), residues: 56 loop : -1.50 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.007 0.001 HIS B 313 PHE 0.025 0.001 PHE A 393 TYR 0.031 0.002 TYR A 399 ARG 0.001 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 4) link_NAG-ASN : angle 1.71249 ( 12) link_BETA1-4 : bond 0.00859 ( 4) link_BETA1-4 : angle 3.09098 ( 12) hydrogen bonds : bond 0.03668 ( 363) hydrogen bonds : angle 4.25758 ( 1068) SS BOND : bond 0.00094 ( 1) SS BOND : angle 1.07828 ( 2) covalent geometry : bond 0.00285 ( 7500) covalent geometry : angle 0.70728 (10228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7440 (p0) REVERT: A 258 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.5574 (mmt) REVERT: A 354 LEU cc_start: 0.7927 (tp) cc_final: 0.7705 (tp) REVERT: A 356 MET cc_start: 0.6476 (mpp) cc_final: 0.6114 (mpp) REVERT: B 158 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (tt) REVERT: B 426 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8049 (t) outliers start: 38 outliers final: 30 residues processed: 194 average time/residue: 0.1918 time to fit residues: 54.3880 Evaluate side-chains 195 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143473 restraints weight = 14061.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143856 restraints weight = 9645.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144943 restraints weight = 7858.834| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7509 Z= 0.125 Angle : 0.737 13.171 10254 Z= 0.339 Chirality : 0.043 0.199 1213 Planarity : 0.004 0.049 1250 Dihedral : 7.567 57.523 1367 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.17 % Allowed : 37.16 % Favored : 58.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 914 helix: 1.70 (0.24), residues: 480 sheet: -0.01 (0.69), residues: 56 loop : -1.49 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 316 HIS 0.009 0.001 HIS B 313 PHE 0.025 0.001 PHE A 433 TYR 0.018 0.001 TYR B 303 ARG 0.001 0.000 ARG B 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 4) link_NAG-ASN : angle 1.75294 ( 12) link_BETA1-4 : bond 0.00810 ( 4) link_BETA1-4 : angle 2.98074 ( 12) hydrogen bonds : bond 0.03629 ( 363) hydrogen bonds : angle 4.23123 ( 1068) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.00155 ( 2) covalent geometry : bond 0.00286 ( 7500) covalent geometry : angle 0.72850 (10228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7436 (p0) REVERT: A 258 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.5550 (mmt) REVERT: A 354 LEU cc_start: 0.7896 (tp) cc_final: 0.7657 (tp) REVERT: A 356 MET cc_start: 0.6467 (mpp) cc_final: 0.6084 (mpp) REVERT: B 158 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8390 (tt) REVERT: B 426 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8012 (t) outliers start: 32 outliers final: 27 residues processed: 186 average time/residue: 0.1483 time to fit residues: 41.4384 Evaluate side-chains 190 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142153 restraints weight = 13858.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142185 restraints weight = 9898.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143283 restraints weight = 7957.922| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7509 Z= 0.136 Angle : 0.739 10.056 10254 Z= 0.342 Chirality : 0.043 0.189 1213 Planarity : 0.004 0.049 1250 Dihedral : 7.549 57.300 1367 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.82 % Allowed : 37.03 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.47 (0.29), residues: 914 helix: 1.68 (0.24), residues: 480 sheet: -0.02 (0.70), residues: 55 loop : -1.50 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 316 HIS 0.008 0.001 HIS B 313 PHE 0.019 0.001 PHE A 393 TYR 0.015 0.001 TYR A 337 ARG 0.001 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 4) link_NAG-ASN : angle 1.78002 ( 12) link_BETA1-4 : bond 0.00760 ( 4) link_BETA1-4 : angle 2.91449 ( 12) hydrogen bonds : bond 0.03710 ( 363) hydrogen bonds : angle 4.26665 ( 1068) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.94270 ( 2) covalent geometry : bond 0.00317 ( 7500) covalent geometry : angle 0.73056 (10228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.37 seconds wall clock time: 53 minutes 14.05 seconds (3194.05 seconds total)