Starting phenix.real_space_refine on Sun May 11 15:53:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8z_42030/05_2025/8u8z_42030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8z_42030/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8z_42030/05_2025/8u8z_42030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8z_42030/05_2025/8u8z_42030.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8z_42030/05_2025/8u8z_42030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8z_42030/05_2025/8u8z_42030.cif" } resolution = 3.25 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= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.29, per 1000 atoms: 0.77 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: 2.00 Conformation dependent library (CDL) restraints added in 911.2 milliseconds 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: 0.88 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: 2.70 Time building geometry restraints manager: 2.33 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 533 or resid 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.250 Find NCS groups from input model: 0.330 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- 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 (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: 0.97 (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 TRP 0.015 0.001 TRP A 476 HIS 0.007 0.001 HIS A 107 PHE 0.061 0.002 PHE A 493 TYR 0.026 0.002 TYR B 212 ARG 0.010 0.001 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.14626 ( 445) hydrogen bonds : angle 5.63865 ( 1260) SS BOND : bond 0.00187 ( 2) SS BOND : angle 2.93532 ( 4) covalent geometry : bond 0.00304 ( 8313) covalent geometry : angle 0.65654 (11305) 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 : 0.983 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: 0.2003 time to fit residues: 29.5089 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 : 0.946 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062727 restraints weight = 23361.302| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.03 r_work: 0.3011 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8317 Z= 0.149 Angle : 0.569 6.560 11309 Z= 0.295 Chirality : 0.042 0.132 1269 Planarity : 0.005 0.053 1479 Dihedral : 6.456 67.597 1166 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.63 % Allowed : 24.72 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1026 helix: 1.72 (0.25), residues: 408 sheet: -0.23 (0.38), residues: 194 loop : -0.38 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 PHE 0.017 0.001 PHE A 34 TYR 0.011 0.001 TYR A 259 ARG 0.007 0.001 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 445) hydrogen bonds : angle 4.80473 ( 1260) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.89998 ( 4) covalent geometry : bond 0.00339 ( 8313) covalent geometry : angle 0.56855 (11305) Misc. bond : bond 0.00082 ( 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 100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8119 (pm20) cc_final: 0.7792 (pm20) REVERT: A 328 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9440 (mt) REVERT: A 451 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7569 (t70) REVERT: A 476 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7918 (t60) REVERT: A 480 MET cc_start: 0.9082 (mmm) cc_final: 0.8749 (mmp) REVERT: B 40 GLU cc_start: 0.8088 (tp30) cc_final: 0.7649 (tp30) outliers start: 32 outliers final: 9 residues processed: 96 average time/residue: 0.1753 time to fit residues: 24.4117 Evaluate side-chains 69 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU 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 308 LEU Chi-restraints excluded: chain A residue 328 ILE 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 368 ILE 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 15 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 0.0010 chunk 34 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.061914 restraints weight = 24321.404| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.28 r_work: 0.3029 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1782 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= 0.109 Angle : 0.514 6.789 11309 Z= 0.265 Chirality : 0.041 0.175 1269 Planarity : 0.004 0.041 1479 Dihedral : 5.989 57.341 1162 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 25.28 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1026 helix: 1.68 (0.25), residues: 410 sheet: -0.15 (0.38), residues: 193 loop : -0.43 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.010 0.001 PHE A 34 TYR 0.009 0.001 TYR A 259 ARG 0.006 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 445) hydrogen bonds : angle 4.63726 ( 1260) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.61871 ( 4) covalent geometry : bond 0.00240 ( 8313) covalent geometry : angle 0.51357 (11305) Misc. bond : bond 0.00124 ( 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 88 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.7844 (mp) cc_final: 0.7565 (mp) REVERT: A 116 GLU cc_start: 0.8220 (pm20) cc_final: 0.7817 (pm20) REVERT: A 316 GLU cc_start: 0.9185 (tp30) cc_final: 0.8932 (tp30) REVERT: A 328 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9438 (mt) REVERT: A 476 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: A 480 MET cc_start: 0.9123 (mmm) cc_final: 0.8807 (mmp) REVERT: B 40 GLU cc_start: 0.8051 (tp30) cc_final: 0.7782 (tp30) outliers start: 21 outliers final: 10 residues processed: 87 average time/residue: 0.1932 time to fit residues: 24.1247 Evaluate side-chains 72 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 62 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 0.0020 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- 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 275 GLN A 404 HIS A 516 GLN B 233 GLN B 241 GLN B 295 HIS B 336 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057288 restraints weight = 24540.856| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 4.19 r_work: 0.2915 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8317 Z= 0.251 Angle : 0.598 5.677 11309 Z= 0.310 Chirality : 0.043 0.144 1269 Planarity : 0.004 0.036 1479 Dihedral : 6.413 58.220 1162 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.76 % Allowed : 23.13 % 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 (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: 0.59 (0.26), residues: 1026 helix: 1.63 (0.25), residues: 415 sheet: -0.14 (0.38), residues: 184 loop : -0.54 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 476 HIS 0.005 0.001 HIS A 30 PHE 0.016 0.002 PHE A 34 TYR 0.013 0.002 TYR B 292 ARG 0.016 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 445) hydrogen bonds : angle 4.77166 ( 1260) SS BOND : bond 0.00394 ( 2) SS BOND : angle 0.63299 ( 4) covalent geometry : bond 0.00571 ( 8313) covalent geometry : angle 0.59784 (11305) Misc. bond : bond 0.00150 ( 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 99 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 57 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8441 (tpp) cc_final: 0.7894 (ttm) REVERT: A 328 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9367 (mt) REVERT: A 451 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7788 (t70) REVERT: A 476 TRP cc_start: 0.8340 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: A 480 MET cc_start: 0.9204 (mmm) cc_final: 0.8971 (mmp) REVERT: A 521 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8261 (mtp85) REVERT: B 40 GLU cc_start: 0.8178 (tp30) cc_final: 0.7778 (tp30) REVERT: B 458 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8704 (mm) outliers start: 42 outliers final: 21 residues processed: 94 average time/residue: 0.1942 time to fit residues: 25.5595 Evaluate side-chains 78 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain A residue 139 MET 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 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 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 294 SER Chi-restraints excluded: chain B residue 337 MET 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 66 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059173 restraints weight = 24128.778| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.13 r_work: 0.2965 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2420 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= 0.124 Angle : 0.533 6.007 11309 Z= 0.273 Chirality : 0.041 0.182 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.208 56.331 1162 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.63 % Allowed : 23.92 % 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 (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: 0.67 (0.26), residues: 1026 helix: 1.77 (0.25), residues: 411 sheet: -0.10 (0.38), residues: 183 loop : -0.57 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.010 0.001 TYR B 292 ARG 0.008 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 445) hydrogen bonds : angle 4.59506 ( 1260) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.66360 ( 4) covalent geometry : bond 0.00276 ( 8313) covalent geometry : angle 0.53187 (11305) Misc. bond : bond 0.00092 ( 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 91 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: A 116 GLU cc_start: 0.8389 (pm20) cc_final: 0.7890 (pm20) REVERT: A 316 GLU cc_start: 0.9168 (tp30) cc_final: 0.8924 (tp30) REVERT: A 328 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9351 (mt) REVERT: A 337 MET cc_start: 0.9035 (ttp) cc_final: 0.8198 (ptm) REVERT: A 451 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7736 (t70) REVERT: A 476 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: A 480 MET cc_start: 0.9209 (mmm) cc_final: 0.8976 (mmp) REVERT: A 521 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8569 (mtp180) REVERT: B 40 GLU cc_start: 0.8132 (tp30) cc_final: 0.7709 (tp30) REVERT: B 458 LEU cc_start: 0.9093 (tp) cc_final: 0.8731 (mm) outliers start: 32 outliers final: 14 residues processed: 89 average time/residue: 0.1833 time to fit residues: 23.4785 Evaluate side-chains 75 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 399 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 22 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.077606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059837 restraints weight = 23827.715| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.96 r_work: 0.2973 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2569 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 : 0.539 7.908 11309 Z= 0.274 Chirality : 0.041 0.174 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.126 57.687 1162 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.17 % Allowed : 24.94 % 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 (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: 0.70 (0.26), residues: 1026 helix: 1.84 (0.25), residues: 411 sheet: -0.07 (0.38), residues: 181 loop : -0.60 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.008 0.001 TYR A 259 ARG 0.006 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 445) hydrogen bonds : angle 4.49689 ( 1260) SS BOND : bond 0.00247 ( 2) SS BOND : angle 1.51015 ( 4) covalent geometry : bond 0.00285 ( 8313) covalent geometry : angle 0.53862 (11305) Misc. bond : bond 0.00083 ( 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 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: A 61 LEU cc_start: 0.8647 (mm) cc_final: 0.8419 (mp) REVERT: A 116 GLU cc_start: 0.8411 (pm20) cc_final: 0.7908 (pm20) REVERT: A 139 MET cc_start: 0.9440 (tmm) cc_final: 0.9044 (tmm) REVERT: A 316 GLU cc_start: 0.9186 (tp30) cc_final: 0.8917 (tp30) REVERT: A 328 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9326 (mt) REVERT: A 337 MET cc_start: 0.9044 (ttp) cc_final: 0.8194 (ptm) REVERT: A 451 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7636 (t70) REVERT: A 476 TRP cc_start: 0.8285 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: A 480 MET cc_start: 0.9211 (mmm) cc_final: 0.8984 (mmp) REVERT: A 521 ARG cc_start: 0.8762 (mtp-110) cc_final: 0.8457 (mtp180) REVERT: B 40 GLU cc_start: 0.8160 (tp30) cc_final: 0.7710 (tp30) REVERT: B 458 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8748 (mm) REVERT: B 480 MET cc_start: 0.8603 (tpp) cc_final: 0.8354 (mmm) outliers start: 28 outliers final: 16 residues processed: 84 average time/residue: 0.1813 time to fit residues: 22.1492 Evaluate side-chains 76 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 87 LEU 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 328 ILE Chi-restraints excluded: chain A residue 375 CYS 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 22 GLN 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 115 LEU 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 61 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 22 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059142 restraints weight = 23925.172| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.95 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8317 Z= 0.146 Angle : 0.546 6.801 11309 Z= 0.279 Chirality : 0.041 0.170 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.157 58.746 1162 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.51 % Allowed : 25.06 % 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 (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: 0.73 (0.26), residues: 1026 helix: 1.87 (0.25), residues: 416 sheet: -0.10 (0.37), residues: 182 loop : -0.60 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE B 23 TYR 0.013 0.001 TYR A 259 ARG 0.006 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 445) hydrogen bonds : angle 4.47094 ( 1260) SS BOND : bond 0.00661 ( 2) SS BOND : angle 1.87023 ( 4) covalent geometry : bond 0.00331 ( 8313) covalent geometry : angle 0.54528 (11305) Misc. bond : bond 0.00085 ( 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 83 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: A 61 LEU cc_start: 0.8664 (mm) cc_final: 0.8440 (mp) REVERT: A 116 GLU cc_start: 0.8441 (pm20) cc_final: 0.7937 (pm20) REVERT: A 139 MET cc_start: 0.9435 (tmm) cc_final: 0.9144 (tmm) REVERT: A 316 GLU cc_start: 0.9194 (tp30) cc_final: 0.8908 (tp30) REVERT: A 328 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9318 (mt) REVERT: A 337 MET cc_start: 0.9073 (ttp) cc_final: 0.8236 (ptm) REVERT: A 451 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7659 (t70) REVERT: A 476 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: A 480 MET cc_start: 0.9212 (mmm) cc_final: 0.8991 (mmp) REVERT: A 521 ARG cc_start: 0.8753 (mtp-110) cc_final: 0.8458 (mtp180) REVERT: B 22 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: B 40 GLU cc_start: 0.8166 (tp30) cc_final: 0.7725 (tp30) REVERT: B 93 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 191 MET cc_start: 0.8898 (tpp) cc_final: 0.8060 (tpp) REVERT: B 458 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8757 (mm) REVERT: B 474 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (pm20) outliers start: 31 outliers final: 18 residues processed: 82 average time/residue: 0.1656 time to fit residues: 20.3582 Evaluate side-chains 77 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 87 LEU 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 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 GLU 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 59 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059481 restraints weight = 23869.332| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.94 r_work: 0.2970 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2755 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 : 0.539 7.250 11309 Z= 0.273 Chirality : 0.042 0.198 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.144 58.706 1162 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.95 % Allowed : 25.51 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1026 helix: 1.91 (0.25), residues: 416 sheet: -0.07 (0.37), residues: 182 loop : -0.62 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.011 0.001 PHE B 23 TYR 0.012 0.001 TYR A 259 ARG 0.006 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 445) hydrogen bonds : angle 4.42983 ( 1260) SS BOND : bond 0.00247 ( 2) SS BOND : angle 1.49521 ( 4) covalent geometry : bond 0.00290 ( 8313) covalent geometry : angle 0.53834 (11305) Misc. bond : bond 0.00077 ( 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 80 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: A 61 LEU cc_start: 0.8676 (mm) cc_final: 0.8463 (mp) REVERT: A 116 GLU cc_start: 0.8425 (pm20) cc_final: 0.7922 (pm20) REVERT: A 139 MET cc_start: 0.9432 (tmm) cc_final: 0.9150 (tmm) REVERT: A 328 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9315 (mt) REVERT: A 337 MET cc_start: 0.9059 (ttp) cc_final: 0.8242 (ptm) REVERT: A 451 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7558 (t70) REVERT: A 476 TRP cc_start: 0.8296 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: A 480 MET cc_start: 0.9214 (mmm) cc_final: 0.9005 (mmp) REVERT: A 521 ARG cc_start: 0.8743 (mtp-110) cc_final: 0.8463 (mtp180) REVERT: B 40 GLU cc_start: 0.8153 (tp30) cc_final: 0.7712 (tp30) REVERT: B 191 MET cc_start: 0.8886 (tpp) cc_final: 0.8060 (tpp) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.1591 time to fit residues: 18.8352 Evaluate side-chains 74 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 87 LEU 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 408 VAL 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 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 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 0.0270 chunk 97 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 22 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.080227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061119 restraints weight = 24654.615| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.18 r_work: 0.3052 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2819 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= 0.100 Angle : 0.522 7.710 11309 Z= 0.262 Chirality : 0.041 0.165 1269 Planarity : 0.004 0.035 1479 Dihedral : 5.919 55.638 1162 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.27 % Allowed : 26.30 % 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 (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: 0.77 (0.26), residues: 1026 helix: 2.01 (0.25), residues: 404 sheet: 0.01 (0.38), residues: 181 loop : -0.67 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 PHE 0.007 0.001 PHE A 102 TYR 0.012 0.001 TYR A 259 ARG 0.005 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 445) hydrogen bonds : angle 4.34744 ( 1260) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.27545 ( 4) covalent geometry : bond 0.00222 ( 8313) covalent geometry : angle 0.52146 (11305) Misc. bond : bond 0.00060 ( 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 80 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: A 116 GLU cc_start: 0.8495 (pm20) cc_final: 0.8005 (pm20) REVERT: A 139 MET cc_start: 0.9399 (tmm) cc_final: 0.9156 (tmm) REVERT: A 316 GLU cc_start: 0.9113 (tp30) cc_final: 0.8901 (tp30) REVERT: A 328 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9352 (mt) REVERT: A 337 MET cc_start: 0.8995 (ttp) cc_final: 0.8202 (ptm) REVERT: A 451 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7555 (t70) REVERT: A 476 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7928 (t60) REVERT: A 521 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8515 (mtp180) REVERT: B 22 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: B 40 GLU cc_start: 0.8091 (tp30) cc_final: 0.7845 (tp30) REVERT: B 98 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 159 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8177 (tp30) REVERT: B 191 MET cc_start: 0.8865 (tpp) cc_final: 0.8091 (tpp) REVERT: B 458 LEU cc_start: 0.9235 (tp) cc_final: 0.8905 (mm) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.1734 time to fit residues: 20.2912 Evaluate side-chains 72 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 87 LEU 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 399 VAL 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 22 GLN Chi-restraints excluded: chain B residue 69 VAL 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 476 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 22 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.079506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060517 restraints weight = 24081.679| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.11 r_work: 0.3040 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2878 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= 0.120 Angle : 0.550 12.449 11309 Z= 0.274 Chirality : 0.041 0.161 1269 Planarity : 0.004 0.035 1479 Dihedral : 5.951 56.472 1162 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.83 % Allowed : 26.53 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1026 helix: 2.03 (0.25), residues: 404 sheet: 0.00 (0.38), residues: 182 loop : -0.64 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.006 0.001 HIS B 144 PHE 0.007 0.001 PHE A 34 TYR 0.016 0.001 TYR A 400 ARG 0.006 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 445) hydrogen bonds : angle 4.35626 ( 1260) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.23195 ( 4) covalent geometry : bond 0.00273 ( 8313) covalent geometry : angle 0.54972 (11305) Misc. bond : bond 0.00067 ( 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 79 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.974 Fit side-chains REVERT: A 45 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: A 116 GLU cc_start: 0.8492 (pm20) cc_final: 0.8013 (pm20) REVERT: A 139 MET cc_start: 0.9383 (tmm) cc_final: 0.9137 (tmm) REVERT: A 316 GLU cc_start: 0.9106 (tp30) cc_final: 0.8882 (tp30) REVERT: A 328 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9354 (mt) REVERT: A 337 MET cc_start: 0.9034 (ttp) cc_final: 0.8229 (ptm) REVERT: A 451 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7463 (t70) REVERT: A 476 TRP cc_start: 0.8301 (OUTLIER) cc_final: 0.7968 (t60) REVERT: B 40 GLU cc_start: 0.8107 (tp30) cc_final: 0.7865 (tp30) REVERT: B 93 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 98 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: B 191 MET cc_start: 0.8878 (tpp) cc_final: 0.8119 (tpp) REVERT: B 458 LEU cc_start: 0.9242 (tp) cc_final: 0.8904 (mm) REVERT: B 480 MET cc_start: 0.8405 (mmm) cc_final: 0.7908 (mmm) outliers start: 25 outliers final: 15 residues processed: 78 average time/residue: 0.1673 time to fit residues: 19.6942 Evaluate side-chains 72 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 87 LEU 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 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL 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 93 LEU Chi-restraints excluded: chain B residue 98 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.079089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059925 restraints weight = 24532.552| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.14 r_work: 0.3025 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8317 Z= 0.128 Angle : 0.554 11.721 11309 Z= 0.276 Chirality : 0.042 0.162 1269 Planarity : 0.004 0.037 1479 Dihedral : 6.047 57.484 1162 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.72 % Allowed : 26.53 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1026 helix: 2.02 (0.25), residues: 404 sheet: 0.02 (0.38), residues: 182 loop : -0.64 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.005 0.001 HIS B 144 PHE 0.007 0.001 PHE A 34 TYR 0.015 0.001 TYR A 259 ARG 0.006 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 445) hydrogen bonds : angle 4.36425 ( 1260) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.21409 ( 4) covalent geometry : bond 0.00291 ( 8313) covalent geometry : angle 0.55374 (11305) Misc. bond : bond 0.00071 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.40 seconds wall clock time: 69 minutes 12.80 seconds (4152.80 seconds total)