Starting phenix.real_space_refine on Fri Aug 22 21:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8z_42030/08_2025/8u8z_42030.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 46 5.16 5 C 5129 2.51 5 N 1431 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4031 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4030 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.13, per 1000 atoms: 0.26 Number of scatterers: 8147 At special positions: 0 Unit cell: (101.178, 81.468, 129.429, 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 46 16.00 O 1541 8.00 N 1431 7.00 C 5129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 379 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 365.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 45.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.538A pdb=" N GLY A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.024A pdb=" N ARG A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.900A pdb=" N ARG A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 340 removed outlier: 4.304A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.597A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 4.021A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.933A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.643A pdb=" N GLU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 488 through 516 Processing helix chain 'A' and resid 517 through 534 removed outlier: 3.513A pdb=" N ARG A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 534 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.515A pdb=" N ASP B 18 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.920A pdb=" N ARG B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.520A pdb=" N ILE B 204 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.874A pdb=" N ARG B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 340 removed outlier: 4.462A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.648A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.957A pdb=" N ALA B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 395 " --> pdb=" O TRP B 391 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.952A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.607A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 488 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.533A pdb=" N VAL A 46 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 33 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.578A pdb=" N GLY A 180 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A 275 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 269 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 449 removed outlier: 3.853A pdb=" N GLN A 444 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.197A pdb=" N ILE B 43 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS B 37 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 33 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.563A pdb=" N GLY B 180 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 275 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 269 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 377 Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 449 removed outlier: 4.007A pdb=" N GLN B 444 " --> pdb=" O MET B 480 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1260 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: 1.31 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1516 1.33 - 1.45: 2006 1.45 - 1.57: 4713 1.57 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 8313 Sorted by residual: bond pdb=" CB THR A 35 " pdb=" CG2 THR A 35 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB ARG B 138 " pdb=" CG ARG B 138 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CB VAL A 431 " pdb=" CG1 VAL A 431 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" CG LEU A 117 " pdb=" CD1 LEU A 117 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 ... (remaining 8308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11018 1.87 - 3.74: 239 3.74 - 5.61: 39 5.61 - 7.48: 8 7.48 - 9.35: 1 Bond angle restraints: 11305 Sorted by residual: angle pdb=" CA GLN B 372 " pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N MET B 136 " pdb=" CA MET B 136 " pdb=" C MET B 136 " ideal model delta sigma weight residual 111.03 114.26 -3.23 1.11e+00 8.12e-01 8.49e+00 angle pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " pdb=" CD GLN B 372 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.70e+00 3.46e-01 7.61e+00 angle pdb=" CA CYS B 375 " pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " ideal model delta sigma weight residual 114.40 108.10 6.30 2.30e+00 1.89e-01 7.51e+00 angle pdb=" CA LEU A 115 " pdb=" CB LEU A 115 " pdb=" CG LEU A 115 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.13e+00 ... (remaining 11300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4283 17.14 - 34.28: 536 34.28 - 51.43: 181 51.43 - 68.57: 55 68.57 - 85.71: 8 Dihedral angle restraints: 5063 sinusoidal: 2065 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual 93.00 45.23 47.77 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sinusoidal sigma weight residual -86.00 -54.14 -31.86 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " pdb=" CG ASP A 347 " pdb=" OD1 ASP A 347 " ideal model delta sinusoidal sigma weight residual -30.00 -89.68 59.68 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 920 0.042 - 0.084: 226 0.084 - 0.126: 104 0.126 - 0.168: 17 0.168 - 0.210: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ARG B 138 " pdb=" N ARG B 138 " pdb=" C ARG B 138 " pdb=" CB ARG B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1266 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 493 " -0.016 2.00e-02 2.50e+03 2.90e-02 1.47e+01 pdb=" CG PHE A 493 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 493 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 493 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 493 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 493 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 493 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 427 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 428 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 427 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 428 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " -0.047 5.00e-02 4.00e+02 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 86 2.65 - 3.21: 7253 3.21 - 3.77: 12656 3.77 - 4.34: 16846 4.34 - 4.90: 28281 Nonbonded interactions: 65122 Sorted by model distance: nonbonded pdb=" OD1 ASN B 135 " pdb=" NH1 ARG B 138 " model vdw 2.082 3.120 nonbonded pdb=" OE1 GLU B 118 " pdb=" OH TYR B 292 " model vdw 2.159 3.040 nonbonded pdb=" OD2 ASP B 203 " pdb=" OH TYR B 259 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 341 " pdb=" OG1 THR A 343 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR B 238 " pdb=" OE1 GLN B 240 " model vdw 2.237 3.040 ... (remaining 65117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 533 or resid 900)) selection = (chain 'B' and resid 12 through 900) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8317 Z= 0.167 Angle : 0.659 9.347 11309 Z= 0.343 Chirality : 0.046 0.210 1269 Planarity : 0.006 0.090 1479 Dihedral : 17.592 85.710 3113 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.91 % Allowed : 28.57 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 1026 helix: 2.04 (0.26), residues: 405 sheet: -0.23 (0.37), residues: 198 loop : -0.23 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 386 TYR 0.026 0.002 TYR B 212 PHE 0.061 0.002 PHE A 493 TRP 0.015 0.001 TRP A 476 HIS 0.007 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8313) covalent geometry : angle 0.65654 (11305) SS BOND : bond 0.00187 ( 2) SS BOND : angle 2.93532 ( 4) hydrogen bonds : bond 0.14626 ( 445) hydrogen bonds : angle 5.63865 ( 1260) Misc. bond : bond 0.06518 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8402 (mp) cc_final: 0.7737 (mp) REVERT: A 337 MET cc_start: 0.8019 (ttp) cc_final: 0.7790 (ttt) outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.0834 time to fit residues: 12.2672 Evaluate side-chains 63 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 69 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 404 HIS ** 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 = 0.3565 r_free = 0.3565 target = 0.080253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060555 restraints weight = 24088.915| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.32 r_work: 0.2965 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8317 Z= 0.187 Angle : 0.588 6.431 11309 Z= 0.306 Chirality : 0.043 0.133 1269 Planarity : 0.005 0.053 1479 Dihedral : 6.474 63.007 1166 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.97 % Allowed : 24.72 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.27), residues: 1026 helix: 1.71 (0.25), residues: 409 sheet: -0.24 (0.38), residues: 195 loop : -0.38 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 521 TYR 0.012 0.001 TYR A 259 PHE 0.018 0.002 PHE A 34 TRP 0.014 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8313) covalent geometry : angle 0.58740 (11305) SS BOND : bond 0.00434 ( 2) SS BOND : angle 0.89252 ( 4) hydrogen bonds : bond 0.04255 ( 445) hydrogen bonds : angle 4.83594 ( 1260) Misc. bond : bond 0.00186 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8128 (pm20) cc_final: 0.7785 (pm20) REVERT: A 328 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9419 (mt) REVERT: A 451 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7609 (t70) REVERT: A 476 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: B 40 GLU cc_start: 0.8129 (tp30) cc_final: 0.7704 (tp30) outliers start: 35 outliers final: 11 residues processed: 98 average time/residue: 0.0726 time to fit residues: 10.3725 Evaluate side-chains 71 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN B 447 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060539 restraints weight = 24014.484| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.22 r_work: 0.2999 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.128 Angle : 0.526 6.710 11309 Z= 0.273 Chirality : 0.041 0.173 1269 Planarity : 0.004 0.041 1479 Dihedral : 6.089 57.378 1162 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 24.60 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1026 helix: 1.66 (0.25), residues: 410 sheet: -0.03 (0.38), residues: 183 loop : -0.46 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 519 TYR 0.013 0.001 TYR B 292 PHE 0.011 0.001 PHE A 34 TRP 0.014 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8313) covalent geometry : angle 0.52604 (11305) SS BOND : bond 0.00303 ( 2) SS BOND : angle 0.66978 ( 4) hydrogen bonds : bond 0.03784 ( 445) hydrogen bonds : angle 4.69151 ( 1260) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8667 (mm) cc_final: 0.8450 (mp) REVERT: A 116 GLU cc_start: 0.8240 (pm20) cc_final: 0.7831 (pm20) REVERT: A 316 GLU cc_start: 0.9193 (tp30) cc_final: 0.8946 (tp30) REVERT: A 328 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9381 (mt) REVERT: A 476 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: B 40 GLU cc_start: 0.8081 (tp30) cc_final: 0.7611 (tp30) outliers start: 29 outliers final: 13 residues processed: 92 average time/residue: 0.0793 time to fit residues: 10.6310 Evaluate side-chains 73 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 0.0050 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 241 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061355 restraints weight = 24052.744| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.02 r_work: 0.3011 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.041 8317 Z= 0.121 Angle : 0.527 6.970 11309 Z= 0.270 Chirality : 0.041 0.178 1269 Planarity : 0.004 0.036 1479 Dihedral : 6.059 57.225 1162 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.85 % Allowed : 23.70 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1026 helix: 1.75 (0.25), residues: 411 sheet: 0.05 (0.39), residues: 183 loop : -0.48 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 521 TYR 0.008 0.001 TYR A 259 PHE 0.010 0.001 PHE A 34 TRP 0.014 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8313) covalent geometry : angle 0.52742 (11305) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.57994 ( 4) hydrogen bonds : bond 0.03557 ( 445) hydrogen bonds : angle 4.59429 ( 1260) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: A 139 MET cc_start: 0.9418 (tmm) cc_final: 0.9115 (tmm) REVERT: A 316 GLU cc_start: 0.9188 (tp30) cc_final: 0.8898 (tp30) REVERT: A 328 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9378 (mt) REVERT: A 451 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7625 (t70) REVERT: A 476 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7854 (m-10) REVERT: A 521 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8779 (mtp180) REVERT: B 40 GLU cc_start: 0.8101 (tp30) cc_final: 0.7840 (tp30) REVERT: B 458 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8736 (mm) outliers start: 34 outliers final: 17 residues processed: 94 average time/residue: 0.0790 time to fit residues: 10.6484 Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 404 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS B 336 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057996 restraints weight = 24419.156| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.20 r_work: 0.2940 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8317 Z= 0.180 Angle : 0.553 6.801 11309 Z= 0.284 Chirality : 0.042 0.170 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.259 58.780 1162 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.54 % Allowed : 23.02 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1026 helix: 1.77 (0.25), residues: 411 sheet: -0.10 (0.38), residues: 184 loop : -0.59 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 519 TYR 0.009 0.001 TYR A 259 PHE 0.013 0.001 PHE A 34 TRP 0.017 0.001 TRP A 476 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8313) covalent geometry : angle 0.55299 (11305) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.59462 ( 4) hydrogen bonds : bond 0.03737 ( 445) hydrogen bonds : angle 4.62550 ( 1260) Misc. bond : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 116 GLU cc_start: 0.8449 (pm20) cc_final: 0.7952 (pm20) REVERT: A 139 MET cc_start: 0.9489 (tmm) cc_final: 0.9131 (tmm) REVERT: A 328 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9343 (mt) REVERT: A 337 MET cc_start: 0.9079 (ttp) cc_final: 0.8218 (ptm) REVERT: A 451 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7688 (t70) REVERT: A 476 TRP cc_start: 0.8285 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: B 40 GLU cc_start: 0.8177 (tp30) cc_final: 0.7743 (tp30) REVERT: B 191 MET cc_start: 0.8885 (tpp) cc_final: 0.8127 (tpp) REVERT: B 458 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8755 (mm) outliers start: 40 outliers final: 23 residues processed: 94 average time/residue: 0.0867 time to fit residues: 11.5410 Evaluate side-chains 83 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** 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 = 0.3511 r_free = 0.3511 target = 0.077688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059924 restraints weight = 23757.617| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.96 r_work: 0.2977 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.127 Angle : 0.532 7.165 11309 Z= 0.270 Chirality : 0.041 0.177 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.135 57.877 1162 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.63 % Allowed : 24.49 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1026 helix: 1.86 (0.25), residues: 411 sheet: -0.04 (0.38), residues: 181 loop : -0.62 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 519 TYR 0.009 0.001 TYR A 259 PHE 0.009 0.001 PHE A 34 TRP 0.015 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8313) covalent geometry : angle 0.53156 (11305) SS BOND : bond 0.00241 ( 2) SS BOND : angle 1.48128 ( 4) hydrogen bonds : bond 0.03476 ( 445) hydrogen bonds : angle 4.51009 ( 1260) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 116 GLU cc_start: 0.8429 (pm20) cc_final: 0.7931 (pm20) REVERT: A 139 MET cc_start: 0.9486 (tmm) cc_final: 0.9141 (tmm) REVERT: A 316 GLU cc_start: 0.9171 (tp30) cc_final: 0.8930 (tp30) REVERT: A 328 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9332 (mt) REVERT: A 337 MET cc_start: 0.9050 (ttp) cc_final: 0.8232 (ptm) REVERT: A 451 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7593 (t70) REVERT: A 476 TRP cc_start: 0.8298 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: A 521 ARG cc_start: 0.8820 (mtp180) cc_final: 0.8241 (mtp85) REVERT: B 40 GLU cc_start: 0.8151 (tp30) cc_final: 0.7711 (tp30) REVERT: B 191 MET cc_start: 0.8891 (tpp) cc_final: 0.8095 (tpp) REVERT: B 458 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 480 MET cc_start: 0.8616 (tpp) cc_final: 0.8363 (mmm) outliers start: 32 outliers final: 18 residues processed: 85 average time/residue: 0.0779 time to fit residues: 9.7765 Evaluate side-chains 78 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.077525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059703 restraints weight = 23979.073| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.98 r_work: 0.2973 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.132 Angle : 0.543 7.302 11309 Z= 0.274 Chirality : 0.041 0.180 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.131 58.583 1162 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.63 % Allowed : 24.26 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1026 helix: 1.89 (0.25), residues: 416 sheet: -0.01 (0.38), residues: 182 loop : -0.63 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.012 0.001 TYR A 259 PHE 0.014 0.001 PHE B 23 TRP 0.015 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8313) covalent geometry : angle 0.54110 (11305) SS BOND : bond 0.00388 ( 2) SS BOND : angle 2.16301 ( 4) hydrogen bonds : bond 0.03467 ( 445) hydrogen bonds : angle 4.47190 ( 1260) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 116 GLU cc_start: 0.8451 (pm20) cc_final: 0.7947 (pm20) REVERT: A 139 MET cc_start: 0.9495 (tmm) cc_final: 0.9082 (tmm) REVERT: A 316 GLU cc_start: 0.9183 (tp30) cc_final: 0.8919 (tp30) REVERT: A 328 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9324 (mt) REVERT: A 337 MET cc_start: 0.9080 (ttp) cc_final: 0.8246 (ptm) REVERT: A 451 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7581 (t70) REVERT: A 476 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: A 480 MET cc_start: 0.9209 (mmp) cc_final: 0.8896 (mmp) REVERT: A 521 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8218 (mtp85) REVERT: B 22 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8021 (mm110) REVERT: B 40 GLU cc_start: 0.8150 (tp30) cc_final: 0.7699 (tp30) REVERT: B 93 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 191 MET cc_start: 0.8882 (tpp) cc_final: 0.8107 (tpp) REVERT: B 458 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 32 outliers final: 21 residues processed: 85 average time/residue: 0.0787 time to fit residues: 9.8168 Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 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 = 0.3524 r_free = 0.3524 target = 0.078278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058839 restraints weight = 24456.557| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.23 r_work: 0.2971 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8317 Z= 0.117 Angle : 0.542 7.333 11309 Z= 0.273 Chirality : 0.041 0.179 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.103 58.366 1162 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.63 % Allowed : 24.60 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1026 helix: 1.94 (0.25), residues: 410 sheet: 0.01 (0.38), residues: 181 loop : -0.64 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 521 TYR 0.012 0.001 TYR A 259 PHE 0.009 0.001 PHE B 23 TRP 0.014 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8313) covalent geometry : angle 0.54080 (11305) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.79159 ( 4) hydrogen bonds : bond 0.03412 ( 445) hydrogen bonds : angle 4.43285 ( 1260) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: A 61 LEU cc_start: 0.8650 (mm) cc_final: 0.8353 (mp) REVERT: A 116 GLU cc_start: 0.8461 (pm20) cc_final: 0.7946 (pm20) REVERT: A 139 MET cc_start: 0.9540 (tmm) cc_final: 0.9162 (tmm) REVERT: A 316 GLU cc_start: 0.9199 (tp30) cc_final: 0.8926 (tp30) REVERT: A 328 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9327 (mt) REVERT: A 337 MET cc_start: 0.9073 (ttp) cc_final: 0.8249 (ptm) REVERT: A 451 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7556 (t70) REVERT: A 476 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: A 521 ARG cc_start: 0.8821 (mtp180) cc_final: 0.8217 (mtp85) REVERT: B 22 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: B 40 GLU cc_start: 0.8134 (tp30) cc_final: 0.7681 (tp30) REVERT: B 98 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: B 191 MET cc_start: 0.8865 (tpp) cc_final: 0.8103 (tpp) REVERT: B 458 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8763 (mm) outliers start: 32 outliers final: 23 residues processed: 83 average time/residue: 0.0735 time to fit residues: 8.8912 Evaluate side-chains 84 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 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 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** B 404 HIS ** 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 = 0.3608 r_free = 0.3608 target = 0.079810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061029 restraints weight = 24293.119| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.08 r_work: 0.3031 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8317 Z= 0.118 Angle : 0.540 7.747 11309 Z= 0.273 Chirality : 0.041 0.176 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.081 58.377 1162 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.63 % Allowed : 24.60 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1026 helix: 1.94 (0.25), residues: 410 sheet: 0.08 (0.38), residues: 182 loop : -0.65 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 521 TYR 0.012 0.001 TYR A 259 PHE 0.009 0.001 PHE B 23 TRP 0.013 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8313) covalent geometry : angle 0.53957 (11305) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.54464 ( 4) hydrogen bonds : bond 0.03377 ( 445) hydrogen bonds : angle 4.41158 ( 1260) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 61 LEU cc_start: 0.8708 (mm) cc_final: 0.8417 (mp) REVERT: A 116 GLU cc_start: 0.8491 (pm20) cc_final: 0.8014 (pm20) REVERT: A 139 MET cc_start: 0.9527 (tmm) cc_final: 0.9152 (tmm) REVERT: A 316 GLU cc_start: 0.9128 (tp30) cc_final: 0.8847 (tp30) REVERT: A 328 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9344 (mt) REVERT: A 337 MET cc_start: 0.9042 (ttp) cc_final: 0.8241 (ptm) REVERT: A 451 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7654 (t70) REVERT: A 476 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7758 (m-10) REVERT: A 521 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8224 (mtp85) REVERT: B 40 GLU cc_start: 0.8092 (tp30) cc_final: 0.7654 (tp30) REVERT: B 93 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 98 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: B 191 MET cc_start: 0.8860 (tpp) cc_final: 0.8136 (tpp) outliers start: 32 outliers final: 23 residues processed: 82 average time/residue: 0.0629 time to fit residues: 7.6946 Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 74 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS B 22 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.080298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061413 restraints weight = 24164.092| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.12 r_work: 0.3062 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8317 Z= 0.101 Angle : 0.532 8.196 11309 Z= 0.267 Chirality : 0.041 0.176 1269 Planarity : 0.004 0.035 1479 Dihedral : 5.937 56.149 1162 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 25.74 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.26), residues: 1026 helix: 1.98 (0.25), residues: 404 sheet: 0.11 (0.38), residues: 181 loop : -0.68 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 521 TYR 0.011 0.001 TYR B 259 PHE 0.007 0.001 PHE A 102 TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8313) covalent geometry : angle 0.53119 (11305) SS BOND : bond 0.00225 ( 2) SS BOND : angle 1.30251 ( 4) hydrogen bonds : bond 0.03213 ( 445) hydrogen bonds : angle 4.34020 ( 1260) Misc. bond : bond 0.00056 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: A 116 GLU cc_start: 0.8434 (pm20) cc_final: 0.7957 (pm20) REVERT: A 139 MET cc_start: 0.9538 (tmm) cc_final: 0.9163 (tmm) REVERT: A 328 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9349 (mt) REVERT: A 337 MET cc_start: 0.9013 (ttp) cc_final: 0.8202 (ptm) REVERT: A 451 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7386 (t70) REVERT: A 476 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: A 521 ARG cc_start: 0.8787 (mtp180) cc_final: 0.8217 (mtp85) REVERT: B 40 GLU cc_start: 0.8072 (tp30) cc_final: 0.7816 (tp30) REVERT: B 93 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 98 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: B 159 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8189 (tp30) REVERT: B 191 MET cc_start: 0.8830 (tpp) cc_final: 0.8144 (tpp) REVERT: B 458 LEU cc_start: 0.9229 (tp) cc_final: 0.8908 (mm) outliers start: 22 outliers final: 15 residues processed: 81 average time/residue: 0.0676 time to fit residues: 7.9774 Evaluate side-chains 73 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** 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 = 0.3595 r_free = 0.3595 target = 0.079741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061178 restraints weight = 24274.427| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.04 r_work: 0.3055 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8317 Z= 0.113 Angle : 0.550 12.064 11309 Z= 0.275 Chirality : 0.041 0.173 1269 Planarity : 0.004 0.035 1479 Dihedral : 5.961 56.810 1162 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.61 % Allowed : 25.96 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.27), residues: 1026 helix: 1.97 (0.25), residues: 403 sheet: 0.11 (0.38), residues: 181 loop : -0.62 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 521 TYR 0.014 0.001 TYR A 259 PHE 0.007 0.001 PHE B 102 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8313) covalent geometry : angle 0.54950 (11305) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.27417 ( 4) hydrogen bonds : bond 0.03280 ( 445) hydrogen bonds : angle 4.33320 ( 1260) Misc. bond : bond 0.00061 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.89 seconds wall clock time: 32 minutes 48.04 seconds (1968.04 seconds total)