Starting phenix.real_space_refine on Fri Sep 11 18:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.cif Found real_map, /net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10aw_75037/09_2026/10aw_75037.map" } resolution = 2.82 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= -0.001 sd= 0.023 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 36 5.16 5 C 6627 2.51 5 N 1809 2.21 5 O 2007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10479 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3493 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain: "B" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3493 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain: "C" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3493 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 423} Time building chain proxies: 2.38, per 1000 atoms: 0.23 Number of scatterers: 10479 At special positions: 0 Unit cell: (97.37, 97.37, 135.89, 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 36 16.00 O 2007 8.00 N 1809 7.00 C 6627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 391.5 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 16.1% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 38 through 78 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.596A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'B' and resid 38 through 78 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.540A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'C' and resid 38 through 78 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.606A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 411 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.625A pdb=" N LYS A 126 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 169 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR A 128 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 167 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG A 130 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 213 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP A 214 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 238 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA A 261 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN A 280 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 323 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 282 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 321 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 284 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 319 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 286 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 317 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS A 288 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 315 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 290 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 313 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 292 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP A 458 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU A 86 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 113 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN A 111 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 90 " --> pdb=" O TRP A 109 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP A 109 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER A 92 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.613A pdb=" N LYS B 126 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU B 169 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR B 128 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 167 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 130 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 213 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP B 214 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 238 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA B 261 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 280 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 323 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 282 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE B 321 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE B 284 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE B 319 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B 286 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA B 317 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N HIS B 288 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR B 315 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B 290 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN B 313 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE B 292 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP B 458 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 86 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 113 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN B 111 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 90 " --> pdb=" O TRP B 109 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP B 109 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER B 92 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.610A pdb=" N LYS C 126 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 169 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 128 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA C 167 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG C 130 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY C 213 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP C 214 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 238 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 261 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 280 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN C 323 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 282 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE C 321 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE C 284 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 319 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 286 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 317 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS C 288 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 315 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C 290 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN C 313 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 292 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP C 458 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU C 86 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 113 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 88 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN C 111 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 90 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP C 109 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 92 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 107 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 210 550 hydrogen bonds defined for protein. 1563 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: 1.86 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3489 1.34 - 1.46: 2270 1.46 - 1.57: 4900 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 10731 Sorted by residual: bond pdb=" N VAL C 308 " pdb=" CA VAL C 308 " ideal model delta sigma weight residual 1.459 1.473 -0.015 1.30e-02 5.92e+03 1.27e+00 bond pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.06e+00 bond pdb=" CA VAL A 308 " pdb=" CB VAL A 308 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.91e-01 bond pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta sigma weight residual 1.480 1.467 0.013 1.71e-02 3.42e+03 5.88e-01 bond pdb=" C GLY B 144 " pdb=" O GLY B 144 " ideal model delta sigma weight residual 1.236 1.229 0.008 1.02e-02 9.61e+03 5.50e-01 ... (remaining 10726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 13230 0.74 - 1.47: 1076 1.47 - 2.21: 150 2.21 - 2.94: 76 2.94 - 3.68: 9 Bond angle restraints: 14541 Sorted by residual: angle pdb=" N GLY C 361 " pdb=" CA GLY C 361 " pdb=" C GLY C 361 " ideal model delta sigma weight residual 111.34 115.02 -3.68 1.82e+00 3.02e-01 4.08e+00 angle pdb=" N GLY A 361 " pdb=" CA GLY A 361 " pdb=" C GLY A 361 " ideal model delta sigma weight residual 111.34 114.99 -3.65 1.82e+00 3.02e-01 4.02e+00 angle pdb=" N PRO A 160 " pdb=" CA PRO A 160 " pdb=" C PRO A 160 " ideal model delta sigma weight residual 114.68 112.62 2.06 1.04e+00 9.25e-01 3.94e+00 angle pdb=" N ALA B 167 " pdb=" CA ALA B 167 " pdb=" C ALA B 167 " ideal model delta sigma weight residual 107.20 110.52 -3.32 1.70e+00 3.46e-01 3.81e+00 angle pdb=" N GLY B 361 " pdb=" CA GLY B 361 " pdb=" C GLY B 361 " ideal model delta sigma weight residual 111.34 114.89 -3.55 1.82e+00 3.02e-01 3.80e+00 ... (remaining 14536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 5839 11.90 - 23.79: 349 23.79 - 35.68: 80 35.68 - 47.58: 30 47.58 - 59.47: 8 Dihedral angle restraints: 6306 sinusoidal: 2502 harmonic: 3804 Sorted by residual: dihedral pdb=" CA LYS A 135 " pdb=" C LYS A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" N GLU A 322 " pdb=" CA GLU A 322 " pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " ideal model delta sinusoidal sigma weight residual -60.00 -119.47 59.47 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS B 135 " pdb=" C LYS B 135 " pdb=" N ASN B 136 " pdb=" CA ASN B 136 " ideal model delta harmonic sigma weight residual 180.00 164.80 15.20 0 5.00e+00 4.00e-02 9.25e+00 ... (remaining 6303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 951 0.027 - 0.054: 344 0.054 - 0.080: 93 0.080 - 0.107: 66 0.107 - 0.134: 43 Chirality restraints: 1497 Sorted by residual: chirality pdb=" CA ILE C 465 " pdb=" N ILE C 465 " pdb=" C ILE C 465 " pdb=" CB ILE C 465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 465 " pdb=" N ILE B 465 " pdb=" C ILE B 465 " pdb=" CB ILE B 465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 465 " pdb=" N ILE A 465 " pdb=" C ILE A 465 " pdb=" CB ILE A 465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1494 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 174 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO B 175 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 174 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 175 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 174 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO C 175 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 175 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 175 " -0.022 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2858 2.81 - 3.33: 8828 3.33 - 3.85: 17023 3.85 - 4.38: 20641 4.38 - 4.90: 37659 Nonbonded interactions: 87009 Sorted by model distance: nonbonded pdb=" O ASN A 411 " pdb=" NH2 ARG A 448 " model vdw 2.283 3.120 nonbonded pdb=" O ASN B 411 " pdb=" NH2 ARG B 448 " model vdw 2.288 3.120 nonbonded pdb=" O ASN C 411 " pdb=" NH2 ARG C 448 " model vdw 2.299 3.120 nonbonded pdb=" OG SER C 88 " pdb=" ND2 ASN C 470 " model vdw 2.304 3.120 nonbonded pdb=" O ILE C 412 " pdb=" OG1 THR C 415 " model vdw 2.305 3.040 ... (remaining 87004 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.002 0.015 10731 Z= 0.117 Angle : 0.459 3.677 14541 Z= 0.277 Chirality : 0.039 0.134 1497 Planarity : 0.003 0.041 1920 Dihedral : 8.989 59.473 3894 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.39 % Allowed : 3.14 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1308 helix: 4.79 (0.32), residues: 174 sheet: 1.93 (0.23), residues: 531 loop : -1.37 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.006 0.001 TYR C 423 PHE 0.009 0.001 PHE B 365 TRP 0.006 0.001 TRP C 242 HIS 0.001 0.000 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (10731) covalent geometry : angle 0.45884 / 0.28 (14541) hydrogen bonds : bond 0.20516 / 13.87 ( 550) hydrogen bonds : angle 8.66350 / 6.17 ( 1563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.7960 (mt0) cc_final: 0.7725 (mt0) REVERT: B 68 ARG cc_start: 0.7214 (mtp180) cc_final: 0.6856 (mtp180) REVERT: B 408 ASP cc_start: 0.7465 (t0) cc_final: 0.7181 (t70) REVERT: B 442 GLN cc_start: 0.7905 (mt0) cc_final: 0.7637 (mt0) REVERT: C 137 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: C 408 ASP cc_start: 0.7583 (t0) cc_final: 0.7297 (t0) REVERT: C 442 GLN cc_start: 0.8012 (mt0) cc_final: 0.7663 (mt0) outliers start: 15 outliers final: 8 residues processed: 164 average time/residue: 0.6930 time to fit residues: 121.4469 Evaluate side-chains 102 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 348 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 332 ASN A 432 GLN A 470 ASN B 36 GLN B 136 ASN B 318 ASN B 332 ASN B 432 GLN C 36 GLN C 136 ASN C 318 ASN C 432 GLN C 470 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091237 restraints weight = 17292.607| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.39 r_work: 0.3169 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10731 Z= 0.150 Angle : 0.527 10.989 14541 Z= 0.288 Chirality : 0.043 0.155 1497 Planarity : 0.004 0.040 1920 Dihedral : 5.425 51.364 1475 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.49 % Allowed : 9.14 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1308 helix: 4.84 (0.32), residues: 156 sheet: 1.75 (0.22), residues: 588 loop : -0.88 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 430 TYR 0.010 0.001 TYR C 399 PHE 0.011 0.001 PHE B 365 TRP 0.007 0.001 TRP B 109 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10731) covalent geometry : angle 0.52725 / 0.29 (14541) hydrogen bonds : bond 0.03752 / 2.52 ( 550) hydrogen bonds : angle 5.89442 / 4.24 ( 1563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: A 132 SER cc_start: 0.9361 (m) cc_final: 0.9029 (m) REVERT: A 390 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 408 ASP cc_start: 0.8049 (t0) cc_final: 0.7787 (t0) REVERT: A 430 ARG cc_start: 0.9118 (ptt90) cc_final: 0.8441 (ptt90) REVERT: B 348 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7536 (p0) REVERT: B 408 ASP cc_start: 0.8020 (t0) cc_final: 0.7703 (t70) REVERT: C 137 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: C 348 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7811 (p0) REVERT: C 390 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: C 408 ASP cc_start: 0.8163 (t0) cc_final: 0.7866 (t70) REVERT: C 461 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7495 (mtp-110) outliers start: 27 outliers final: 7 residues processed: 112 average time/residue: 0.6990 time to fit residues: 83.8425 Evaluate side-chains 95 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN A 332 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 332 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087469 restraints weight = 17394.483| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.44 r_work: 0.3131 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10731 Z= 0.239 Angle : 0.586 13.220 14541 Z= 0.315 Chirality : 0.045 0.185 1497 Planarity : 0.004 0.046 1920 Dihedral : 5.687 54.216 1472 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.49 % Allowed : 10.16 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.24), residues: 1308 helix: 4.49 (0.35), residues: 156 sheet: 1.66 (0.22), residues: 582 loop : -0.95 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 166 TYR 0.012 0.002 TYR C 220 PHE 0.012 0.002 PHE B 284 TRP 0.010 0.001 TRP A 109 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (10731) covalent geometry : angle 0.58566 / 0.31 (14541) hydrogen bonds : bond 0.03687 / 2.44 ( 550) hydrogen bonds : angle 5.49325 / 3.96 ( 1563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.406 Fit side-chains REVERT: A 68 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8612 (mtp180) REVERT: A 390 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: A 408 ASP cc_start: 0.8151 (t0) cc_final: 0.7805 (t0) REVERT: B 68 ARG cc_start: 0.8895 (mtp180) cc_final: 0.8679 (mtp180) REVERT: B 110 MET cc_start: 0.8900 (mtm) cc_final: 0.8602 (mmt) REVERT: B 408 ASP cc_start: 0.8028 (t0) cc_final: 0.7692 (t70) REVERT: C 68 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8543 (mtp180) REVERT: C 137 TRP cc_start: 0.8919 (OUTLIER) cc_final: 0.8586 (m-10) REVERT: C 390 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: C 408 ASP cc_start: 0.8244 (t0) cc_final: 0.7945 (t70) outliers start: 27 outliers final: 15 residues processed: 104 average time/residue: 0.7027 time to fit residues: 78.1565 Evaluate side-chains 93 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.0270 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 55 ASN ** 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 = 0.3681 r_free = 0.3681 target = 0.115421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091484 restraints weight = 17075.860| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.35 r_work: 0.3203 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10731 Z= 0.097 Angle : 0.500 13.344 14541 Z= 0.264 Chirality : 0.042 0.168 1497 Planarity : 0.003 0.038 1920 Dihedral : 5.363 52.726 1472 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.95 % Allowed : 9.14 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1308 helix: 4.15 (0.36), residues: 156 sheet: 1.63 (0.21), residues: 582 loop : -0.81 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 430 TYR 0.016 0.001 TYR C 399 PHE 0.006 0.001 PHE B 433 TRP 0.009 0.001 TRP A 242 HIS 0.002 0.000 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (10731) covalent geometry : angle 0.49962 / 0.26 (14541) hydrogen bonds : bond 0.03006 / 1.98 ( 550) hydrogen bonds : angle 4.96299 / 3.53 ( 1563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 390 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: A 408 ASP cc_start: 0.8056 (t0) cc_final: 0.7595 (t0) REVERT: B 133 MET cc_start: 0.8815 (tmm) cc_final: 0.8360 (tmt) REVERT: B 408 ASP cc_start: 0.7969 (t0) cc_final: 0.7644 (t70) REVERT: C 68 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8607 (mtp180) REVERT: C 137 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: C 390 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: C 408 ASP cc_start: 0.8130 (t0) cc_final: 0.7819 (t0) REVERT: C 461 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7453 (mtp-110) outliers start: 32 outliers final: 14 residues processed: 116 average time/residue: 0.6760 time to fit residues: 84.0331 Evaluate side-chains 97 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 285 ASN B 318 ASN B 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090972 restraints weight = 17018.315| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.36 r_work: 0.3192 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10731 Z= 0.118 Angle : 0.523 13.041 14541 Z= 0.272 Chirality : 0.042 0.136 1497 Planarity : 0.004 0.038 1920 Dihedral : 5.374 59.966 1472 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.86 % Allowed : 9.70 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1308 helix: 4.13 (0.36), residues: 156 sheet: 1.59 (0.21), residues: 582 loop : -0.80 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.017 0.001 TYR C 399 PHE 0.007 0.001 PHE B 284 TRP 0.007 0.001 TRP C 242 HIS 0.001 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10731) covalent geometry : angle 0.52346 / 0.27 (14541) hydrogen bonds : bond 0.03044 / 2.00 ( 550) hydrogen bonds : angle 4.83697 / 3.42 ( 1563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 SER cc_start: 0.9321 (m) cc_final: 0.9090 (t) REVERT: A 390 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: A 408 ASP cc_start: 0.8153 (t0) cc_final: 0.7618 (t0) REVERT: B 408 ASP cc_start: 0.7940 (t0) cc_final: 0.7592 (t70) REVERT: C 137 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: C 390 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: C 408 ASP cc_start: 0.8132 (t0) cc_final: 0.7819 (t0) outliers start: 31 outliers final: 15 residues processed: 111 average time/residue: 0.6722 time to fit residues: 80.0763 Evaluate side-chains 92 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 390 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.0170 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 332 ASN C 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089030 restraints weight = 17371.853| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.44 r_work: 0.3148 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10731 Z= 0.183 Angle : 0.569 13.648 14541 Z= 0.297 Chirality : 0.043 0.135 1497 Planarity : 0.004 0.039 1920 Dihedral : 5.382 54.571 1470 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.32 % Allowed : 10.06 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1308 helix: 4.12 (0.37), residues: 156 sheet: 1.51 (0.21), residues: 582 loop : -0.82 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.019 0.001 TYR C 399 PHE 0.011 0.001 PHE B 284 TRP 0.008 0.001 TRP B 109 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (10731) covalent geometry : angle 0.56873 / 0.30 (14541) hydrogen bonds : bond 0.03239 / 2.13 ( 550) hydrogen bonds : angle 4.95712 / 3.50 ( 1563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 390 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: A 408 ASP cc_start: 0.8228 (t0) cc_final: 0.7775 (t0) REVERT: B 110 MET cc_start: 0.8881 (mtm) cc_final: 0.8571 (mmt) REVERT: B 408 ASP cc_start: 0.7990 (t0) cc_final: 0.7652 (t70) REVERT: C 390 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: C 408 ASP cc_start: 0.8194 (t0) cc_final: 0.7891 (t0) outliers start: 36 outliers final: 18 residues processed: 110 average time/residue: 0.6448 time to fit residues: 76.2330 Evaluate side-chains 95 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 332 ASN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 285 ASN B 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087708 restraints weight = 17582.751| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.43 r_work: 0.3120 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 10731 Z= 0.275 Angle : 0.629 13.949 14541 Z= 0.332 Chirality : 0.045 0.137 1497 Planarity : 0.004 0.044 1920 Dihedral : 5.760 56.385 1470 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.86 % Allowed : 10.53 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1308 helix: 4.15 (0.37), residues: 156 sheet: 1.50 (0.21), residues: 567 loop : -1.01 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.017 0.002 TYR C 399 PHE 0.015 0.002 PHE B 284 TRP 0.010 0.002 TRP B 445 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (10731) covalent geometry : angle 0.62910 / 0.33 (14541) hydrogen bonds : bond 0.03556 / 2.35 ( 550) hydrogen bonds : angle 5.17243 / 3.65 ( 1563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8251 (tt0) REVERT: A 390 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: A 408 ASP cc_start: 0.8329 (t0) cc_final: 0.7868 (t70) REVERT: B 110 MET cc_start: 0.8920 (mtm) cc_final: 0.8590 (mmt) REVERT: B 408 ASP cc_start: 0.8040 (t0) cc_final: 0.7700 (t70) REVERT: C 390 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: C 408 ASP cc_start: 0.8240 (t0) cc_final: 0.7894 (t70) outliers start: 31 outliers final: 20 residues processed: 105 average time/residue: 0.6520 time to fit residues: 73.6035 Evaluate side-chains 96 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.0070 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 332 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091122 restraints weight = 17015.692| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.36 r_work: 0.3184 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10731 Z= 0.107 Angle : 0.554 14.811 14541 Z= 0.284 Chirality : 0.042 0.134 1497 Planarity : 0.004 0.039 1920 Dihedral : 5.364 56.881 1470 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 12.00 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1308 helix: 4.08 (0.37), residues: 156 sheet: 1.53 (0.21), residues: 567 loop : -0.93 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.019 0.001 TYR C 399 PHE 0.007 0.001 PHE B 433 TRP 0.011 0.001 TRP C 242 HIS 0.001 0.000 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (10731) covalent geometry : angle 0.55419 / 0.28 (14541) hydrogen bonds : bond 0.02999 / 1.99 ( 550) hydrogen bonds : angle 4.82924 / 3.39 ( 1563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8274 (tt0) REVERT: A 390 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 408 ASP cc_start: 0.8048 (t0) cc_final: 0.7567 (t0) REVERT: B 408 ASP cc_start: 0.7923 (t0) cc_final: 0.7584 (t70) REVERT: C 390 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: C 408 ASP cc_start: 0.8118 (t0) cc_final: 0.7798 (t0) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.6889 time to fit residues: 73.8450 Evaluate side-chains 90 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090990 restraints weight = 17300.706| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.41 r_work: 0.3111 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10731 Z= 0.147 Angle : 0.581 15.077 14541 Z= 0.298 Chirality : 0.042 0.131 1497 Planarity : 0.004 0.039 1920 Dihedral : 5.162 54.900 1468 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.66 % Allowed : 12.65 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1308 helix: 4.08 (0.37), residues: 156 sheet: 1.51 (0.21), residues: 573 loop : -0.89 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.022 0.001 TYR C 399 PHE 0.008 0.001 PHE B 284 TRP 0.009 0.001 TRP C 242 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10731) covalent geometry : angle 0.58055 / 0.30 (14541) hydrogen bonds : bond 0.03080 / 2.02 ( 550) hydrogen bonds : angle 4.83899 / 3.40 ( 1563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8243 (tt0) REVERT: A 390 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: A 408 ASP cc_start: 0.8017 (t0) cc_final: 0.7540 (t0) REVERT: B 408 ASP cc_start: 0.7928 (t0) cc_final: 0.7568 (t70) REVERT: C 390 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: C 408 ASP cc_start: 0.8117 (t0) cc_final: 0.7797 (t0) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.6752 time to fit residues: 67.9916 Evaluate side-chains 92 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 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 = 0.3675 r_free = 0.3675 target = 0.116703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092036 restraints weight = 17155.411| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.41 r_work: 0.3125 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10731 Z= 0.124 Angle : 0.569 15.436 14541 Z= 0.290 Chirality : 0.042 0.132 1497 Planarity : 0.004 0.039 1920 Dihedral : 5.094 54.848 1468 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.48 % Allowed : 12.93 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1308 helix: 4.08 (0.37), residues: 156 sheet: 1.54 (0.21), residues: 564 loop : -0.94 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.022 0.001 TYR C 399 PHE 0.007 0.001 PHE B 433 TRP 0.010 0.001 TRP C 242 HIS 0.001 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10731) covalent geometry : angle 0.56930 / 0.29 (14541) hydrogen bonds : bond 0.02975 / 1.95 ( 550) hydrogen bonds : angle 4.76254 / 3.35 ( 1563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8235 (tt0) REVERT: A 390 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 408 ASP cc_start: 0.7996 (t0) cc_final: 0.7493 (t0) REVERT: B 408 ASP cc_start: 0.7933 (t0) cc_final: 0.7550 (t70) REVERT: C 390 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: C 408 ASP cc_start: 0.8063 (t0) cc_final: 0.7742 (t0) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.6946 time to fit residues: 69.1033 Evaluate side-chains 92 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN C 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089312 restraints weight = 17648.039| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.42 r_work: 0.3085 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10731 Z= 0.216 Angle : 0.627 17.159 14541 Z= 0.324 Chirality : 0.044 0.134 1497 Planarity : 0.004 0.040 1920 Dihedral : 5.415 55.536 1468 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.66 % Allowed : 12.83 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1308 helix: 4.08 (0.37), residues: 156 sheet: 1.47 (0.21), residues: 573 loop : -0.96 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.024 0.001 TYR C 399 PHE 0.012 0.001 PHE B 284 TRP 0.008 0.001 TRP C 242 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (10731) covalent geometry : angle 0.62678 / 0.32 (14541) hydrogen bonds : bond 0.03365 / 2.21 ( 550) hydrogen bonds : angle 5.00193 / 3.52 ( 1563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3850.30 seconds wall clock time: 66 minutes 30.76 seconds (3990.76 seconds total)