Starting phenix.real_space_refine on Thu Jul 2 02:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gv3_34282/07_2026/8gv3_34282.map" } resolution = 3.05 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= -0.002 sd= 0.238 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 46 5.16 5 C 3634 2.51 5 N 954 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} Conformer: "B" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} bond proxies already assigned to first conformer: 2822 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' ZN': 2, 'NAD': 1, 'WKZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 696 SG CYS A 96 83.998 27.246 17.420 1.00 53.43 S ATOM 715 SG CYS A 99 80.541 26.704 19.076 1.00 59.54 S ATOM 741 SG CYS A 102 81.036 29.728 17.005 1.00 49.33 S ATOM 802 SG CYS A 110 82.922 29.536 20.183 1.00 47.97 S ATOM 323 SG CYS A 44 83.107 47.740 31.478 1.00 59.70 S ATOM 1275 SG CYS A 173 81.944 45.551 28.014 1.00 47.81 S Restraints were copied for chains: B Time building chain proxies: 2.16, per 1000 atoms: 0.38 Number of scatterers: 5720 At special positions: 0 Unit cell: (122.1, 75.9, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 4 15.00 O 1078 8.00 N 954 7.00 C 3634 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: 0.34 Conformation dependent library (CDL) restraints added in 554.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 102 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 99 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 96 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 173 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 44 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 66 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 102 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 99 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 96 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 173 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 44 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 66 " Number of angles added : 12 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 34.3% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.778A pdb=" N ALA A 48 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.665A pdb=" N LYS A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.582A pdb=" N THR A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 303 through 309 removed outlier: 4.053A pdb=" N LEU A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 336 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.661A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.778A pdb=" N ALA B 48 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.666A pdb=" N LYS B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.582A pdb=" N THR B 177 " --> pdb=" O CYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 303 through 309 removed outlier: 4.054A pdb=" N LEU B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 322 through 336 Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.663A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.292A pdb=" N PHE A 129 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 3.802A pdb=" N SER A 74 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS A 37 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 72 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 39 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY A 70 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR A 41 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY A 68 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY A 68 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 152 removed outlier: 7.599A pdb=" N VAL A 370 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN A 348 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 372 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A 350 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.493A pdb=" N ILE A 218 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE A 240 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 220 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 193 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE A 265 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 195 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.291A pdb=" N PHE B 129 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.799A pdb=" N SER B 74 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 37 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 72 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 39 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY B 70 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B 41 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 68 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY B 68 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 152 removed outlier: 7.603A pdb=" N VAL B 370 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 348 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS B 372 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER B 350 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 240 removed outlier: 6.490A pdb=" N ILE B 218 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE B 240 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY B 220 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 193 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE B 265 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 195 " --> pdb=" O PHE B 265 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 562 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: 0.79 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 958 1.31 - 1.43: 1399 1.43 - 1.56: 3393 1.56 - 1.68: 28 1.68 - 1.81: 58 Bond restraints: 5836 Sorted by residual: bond pdb=" C3B NAD A 403 " pdb=" C4B NAD A 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C3B NAD B 403 " pdb=" C4B NAD B 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1B NAD B 403 " pdb=" C2B NAD B 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1B NAD A 403 " pdb=" C2B NAD A 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAD A 403 " pdb=" C2D NAD A 403 " ideal model delta sigma weight residual 1.528 1.269 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 5831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 7820 3.58 - 7.15: 74 7.15 - 10.73: 16 10.73 - 14.30: 4 14.30 - 17.88: 4 Bond angle restraints: 7918 Sorted by residual: angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C4A NAD B 403 " ideal model delta sigma weight residual 126.46 108.58 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C4A NAD A 403 " ideal model delta sigma weight residual 126.46 108.60 17.86 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C8A NAD B 403 " ideal model delta sigma weight residual 127.40 142.77 -15.37 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C8A NAD A 403 " ideal model delta sigma weight residual 127.40 142.71 -15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1A NAD A 403 " pdb=" PA NAD A 403 " pdb=" O2A NAD A 403 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 ... (remaining 7913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3074 17.69 - 35.38: 284 35.38 - 53.07: 64 53.07 - 70.75: 8 70.75 - 88.44: 16 Dihedral angle restraints: 3446 sinusoidal: 1348 harmonic: 2098 Sorted by residual: dihedral pdb=" CA LYS A 322 " pdb=" C LYS A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LYS B 322 " pdb=" C LYS B 322 " pdb=" N SER B 323 " pdb=" CA SER B 323 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA THR A 312 " pdb=" C THR A 312 " pdb=" N TRP A 313 " pdb=" CA TRP A 313 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 3443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 697 0.060 - 0.119: 187 0.119 - 0.179: 20 0.179 - 0.239: 2 0.239 - 0.298: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" C3D NAD A 403 " pdb=" C2D NAD A 403 " pdb=" C4D NAD A 403 " pdb=" O3D NAD A 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3D NAD B 403 " pdb=" C2D NAD B 403 " pdb=" C4D NAD B 403 " pdb=" O3D NAD B 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3B NAD A 403 " pdb=" C2B NAD A 403 " pdb=" C4B NAD A 403 " pdb=" O3B NAD A 403 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 905 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 313 " -0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP B 313 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 313 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 313 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 313 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP A 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 373 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ILE A 373 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE A 373 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 374 " 0.010 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 643 2.75 - 3.28: 5180 3.28 - 3.82: 8564 3.82 - 4.36: 10822 4.36 - 4.90: 19145 Nonbonded interactions: 44354 Sorted by model distance: nonbonded pdb=" OD2 ASP B 124 " pdb=" NH2 ARG B 128 " model vdw 2.208 3.120 nonbonded pdb=" OD2 ASP A 124 " pdb=" NH2 ARG A 128 " model vdw 2.209 3.120 nonbonded pdb=" O CYS A 173 " pdb=" OG1 THR A 177 " model vdw 2.223 3.040 nonbonded pdb=" O CYS B 173 " pdb=" OG1 THR B 177 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP B 222 " pdb=" N ILE B 223 " model vdw 2.265 3.120 ... (remaining 44349 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.50 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.017 0.270 5850 Z= 0.799 Angle : 1.030 17.881 7930 Z= 0.442 Chirality : 0.055 0.298 908 Planarity : 0.005 0.044 992 Dihedral : 15.421 88.441 2110 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.10 (0.29), residues: 744 helix: -0.80 (0.33), residues: 220 sheet: 0.35 (0.44), residues: 140 loop : -1.05 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 35 TYR 0.014 0.002 TYR A 179 PHE 0.017 0.002 PHE B 351 TRP 0.040 0.004 TRP A 313 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.01660 / 0.80 ( 5836) covalent geometry : angle 1.02277 / 0.44 ( 7918) hydrogen bonds : bond 0.20785 / 14.01 ( 202) hydrogen bonds : angle 6.62068 / 4.63 ( 562) metal coordination : bond 0.00737 / 0.52 ( 14) metal coordination : angle 3.27675 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.209 Fit side-chains REVERT: A 365 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7740 (tppt) REVERT: B 233 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 365 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7734 (tppt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0682 time to fit residues: 7.5921 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107119 restraints weight = 13882.035| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.19 r_work: 0.2957 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5850 Z= 0.122 Angle : 0.543 5.375 7930 Z= 0.274 Chirality : 0.046 0.130 908 Planarity : 0.004 0.037 992 Dihedral : 10.990 88.969 828 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.66 % Allowed : 5.15 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.30), residues: 744 helix: -0.23 (0.34), residues: 230 sheet: 0.42 (0.44), residues: 140 loop : -0.94 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.011 0.001 TYR B 179 PHE 0.005 0.001 PHE B 234 TRP 0.020 0.002 TRP A 313 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 5836) covalent geometry : angle 0.53384 / 0.27 ( 7918) hydrogen bonds : bond 0.03953 / 2.68 ( 202) hydrogen bonds : angle 4.83139 / 3.41 ( 562) metal coordination : bond 0.00283 / 0.17 ( 14) metal coordination : angle 2.63108 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.214 Fit side-chains REVERT: A 365 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7163 (tppt) REVERT: B 365 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7197 (tppt) outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.0807 time to fit residues: 8.4091 Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain B residue 313 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107871 restraints weight = 8166.680| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.49 r_work: 0.3007 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5850 Z= 0.136 Angle : 0.534 5.448 7930 Z= 0.270 Chirality : 0.046 0.131 908 Planarity : 0.004 0.037 992 Dihedral : 10.759 89.420 828 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.83 % Allowed : 7.14 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.30), residues: 744 helix: -0.01 (0.34), residues: 230 sheet: 0.24 (0.43), residues: 140 loop : -0.90 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.010 0.001 TYR B 179 PHE 0.005 0.001 PHE A 197 TRP 0.024 0.002 TRP B 313 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 5836) covalent geometry : angle 0.52334 / 0.27 ( 7918) hydrogen bonds : bond 0.04071 / 2.73 ( 202) hydrogen bonds : angle 4.57610 / 3.23 ( 562) metal coordination : bond 0.00405 / 0.24 ( 14) metal coordination : angle 2.72526 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.128 Fit side-chains REVERT: A 365 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7205 (tppt) REVERT: B 365 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7236 (tppt) outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.0724 time to fit residues: 7.0491 Evaluate side-chains 75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.146631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110895 restraints weight = 9776.661| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.76 r_work: 0.3026 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5850 Z= 0.087 Angle : 0.477 5.036 7930 Z= 0.239 Chirality : 0.044 0.124 908 Planarity : 0.004 0.035 992 Dihedral : 10.481 88.308 828 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.83 % Allowed : 7.81 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.30), residues: 744 helix: 0.35 (0.35), residues: 230 sheet: 0.30 (0.43), residues: 140 loop : -0.85 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.008 0.001 TYR A 179 PHE 0.002 0.000 PHE A 318 TRP 0.022 0.002 TRP A 313 HIS 0.002 0.000 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 5836) covalent geometry : angle 0.47025 / 0.24 ( 7918) hydrogen bonds : bond 0.02880 / 1.93 ( 202) hydrogen bonds : angle 4.31006 / 3.07 ( 562) metal coordination : bond 0.00178 / 0.10 ( 14) metal coordination : angle 2.17512 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.122 Fit side-chains REVERT: A 365 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7190 (tppt) REVERT: B 365 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7211 (tppt) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.0660 time to fit residues: 6.2273 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111186 restraints weight = 14190.614| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.61 r_work: 0.2960 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5850 Z= 0.113 Angle : 0.494 5.146 7930 Z= 0.248 Chirality : 0.045 0.131 908 Planarity : 0.004 0.035 992 Dihedral : 10.349 87.610 828 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.00 % Allowed : 7.81 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.30), residues: 744 helix: 0.41 (0.35), residues: 230 sheet: 0.22 (0.42), residues: 140 loop : -0.86 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.009 0.001 TYR B 179 PHE 0.005 0.001 PHE A 197 TRP 0.023 0.002 TRP A 313 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 ( 5836) covalent geometry : angle 0.48566 / 0.25 ( 7918) hydrogen bonds : bond 0.03451 / 2.31 ( 202) hydrogen bonds : angle 4.30632 / 3.05 ( 562) metal coordination : bond 0.00311 / 0.19 ( 14) metal coordination : angle 2.41119 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.134 Fit side-chains REVERT: A 365 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7189 (tppt) REVERT: B 365 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7193 (tppt) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.0661 time to fit residues: 6.2194 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111070 restraints weight = 13098.019| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.11 r_work: 0.3015 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5850 Z= 0.092 Angle : 0.473 4.942 7930 Z= 0.236 Chirality : 0.044 0.127 908 Planarity : 0.004 0.034 992 Dihedral : 10.125 86.244 828 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.00 % Allowed : 7.81 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.30), residues: 744 helix: 0.56 (0.36), residues: 230 sheet: 0.30 (0.43), residues: 140 loop : -0.85 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.008 0.001 TYR B 179 PHE 0.003 0.001 PHE B 197 TRP 0.022 0.002 TRP B 313 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 5836) covalent geometry : angle 0.46516 / 0.24 ( 7918) hydrogen bonds : bond 0.03014 / 2.01 ( 202) hydrogen bonds : angle 4.23627 / 3.00 ( 562) metal coordination : bond 0.00212 / 0.12 ( 14) metal coordination : angle 2.21655 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.208 Fit side-chains REVERT: A 365 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7182 (tppt) REVERT: B 365 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7186 (tppt) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.0645 time to fit residues: 6.0426 Evaluate side-chains 72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103998 restraints weight = 15446.310| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.85 r_work: 0.2869 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5850 Z= 0.238 Angle : 0.617 5.826 7930 Z= 0.314 Chirality : 0.050 0.149 908 Planarity : 0.005 0.037 992 Dihedral : 10.541 87.246 828 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.33 % Allowed : 7.97 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.30), residues: 744 helix: 0.16 (0.35), residues: 230 sheet: -0.03 (0.42), residues: 140 loop : -1.06 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.015 0.002 TYR B 179 PHE 0.011 0.002 PHE B 197 TRP 0.028 0.003 TRP B 313 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.24 ( 5836) covalent geometry : angle 0.60370 / 0.31 ( 7918) hydrogen bonds : bond 0.05396 / 3.64 ( 202) hydrogen bonds : angle 4.65318 / 3.25 ( 562) metal coordination : bond 0.00722 / 0.47 ( 14) metal coordination : angle 3.34435 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.155 Fit side-chains REVERT: A 365 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7227 (tppt) REVERT: B 365 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7223 (tppt) outliers start: 8 outliers final: 8 residues processed: 74 average time/residue: 0.0838 time to fit residues: 8.1766 Evaluate side-chains 72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.143044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107508 restraints weight = 9755.906| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.70 r_work: 0.2983 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5850 Z= 0.145 Angle : 0.537 5.509 7930 Z= 0.270 Chirality : 0.047 0.133 908 Planarity : 0.004 0.037 992 Dihedral : 10.459 87.096 828 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.33 % Allowed : 9.63 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.30), residues: 744 helix: 0.30 (0.35), residues: 230 sheet: 0.01 (0.43), residues: 140 loop : -1.05 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.015 0.001 TYR A 179 PHE 0.006 0.001 PHE B 197 TRP 0.025 0.002 TRP A 313 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 5836) covalent geometry : angle 0.52654 / 0.27 ( 7918) hydrogen bonds : bond 0.03981 / 2.68 ( 202) hydrogen bonds : angle 4.45405 / 3.12 ( 562) metal coordination : bond 0.00404 / 0.26 ( 14) metal coordination : angle 2.79699 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.218 Fit side-chains REVERT: A 160 ASP cc_start: 0.7195 (t0) cc_final: 0.6862 (t70) REVERT: A 365 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7221 (tppt) REVERT: B 160 ASP cc_start: 0.7174 (t0) cc_final: 0.6847 (t70) REVERT: B 365 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7201 (tppt) outliers start: 8 outliers final: 8 residues processed: 74 average time/residue: 0.0835 time to fit residues: 8.1867 Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110808 restraints weight = 9380.807| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.64 r_work: 0.3021 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5850 Z= 0.093 Angle : 0.482 5.009 7930 Z= 0.241 Chirality : 0.045 0.124 908 Planarity : 0.004 0.035 992 Dihedral : 10.042 84.497 828 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.33 % Allowed : 9.63 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.30), residues: 744 helix: 0.53 (0.35), residues: 230 sheet: 0.14 (0.43), residues: 140 loop : -0.98 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.009 0.001 TYR B 179 PHE 0.003 0.001 PHE A 197 TRP 0.023 0.002 TRP A 313 HIS 0.002 0.000 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 ( 5836) covalent geometry : angle 0.47407 / 0.24 ( 7918) hydrogen bonds : bond 0.02982 / 2.00 ( 202) hydrogen bonds : angle 4.24708 / 3.01 ( 562) metal coordination : bond 0.00193 / 0.11 ( 14) metal coordination : angle 2.32241 / 1.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.211 Fit side-chains REVERT: A 365 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7233 (tppt) REVERT: B 365 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7227 (tppt) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.0852 time to fit residues: 8.0687 Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.147632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113910 restraints weight = 8154.275| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.41 r_work: 0.3077 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5850 Z= 0.083 Angle : 0.465 4.639 7930 Z= 0.232 Chirality : 0.044 0.123 908 Planarity : 0.004 0.034 992 Dihedral : 9.310 78.606 828 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.16 % Allowed : 10.13 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.30), residues: 744 helix: 0.68 (0.36), residues: 226 sheet: 0.18 (0.43), residues: 140 loop : -0.87 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.008 0.001 TYR A 179 PHE 0.002 0.000 PHE A 101 TRP 0.021 0.002 TRP A 313 HIS 0.002 0.000 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 ( 5836) covalent geometry : angle 0.45764 / 0.23 ( 7918) hydrogen bonds : bond 0.02701 / 1.80 ( 202) hydrogen bonds : angle 4.13502 / 2.94 ( 562) metal coordination : bond 0.00205 / 0.12 ( 14) metal coordination : angle 2.20498 / 1.45 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.217 Fit side-chains REVERT: A 365 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7257 (tppt) REVERT: B 365 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7263 (tppt) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.0721 time to fit residues: 7.5118 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.0020 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 49 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.148767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113108 restraints weight = 15110.616| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.83 r_work: 0.2998 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5850 Z= 0.077 Angle : 0.457 4.683 7930 Z= 0.226 Chirality : 0.044 0.128 908 Planarity : 0.004 0.032 992 Dihedral : 8.258 68.867 828 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.66 % Allowed : 10.63 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.30), residues: 744 helix: 0.81 (0.36), residues: 226 sheet: 0.31 (0.43), residues: 140 loop : -0.79 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.007 0.001 TYR B 92 PHE 0.002 0.000 PHE A 101 TRP 0.021 0.002 TRP A 313 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 ( 5836) covalent geometry : angle 0.44870 / 0.23 ( 7918) hydrogen bonds : bond 0.02493 / 1.66 ( 202) hydrogen bonds : angle 4.04906 / 2.88 ( 562) metal coordination : bond 0.00182 / 0.10 ( 14) metal coordination : angle 2.24342 / 1.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.29 seconds wall clock time: 24 minutes 0.96 seconds (1440.96 seconds total)