Starting phenix.real_space_refine on Wed Jun 3 13:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gv3_34282/06_2026/8gv3_34282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gv3_34282/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gv3_34282/06_2026/8gv3_34282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gv3_34282/06_2026/8gv3_34282.map" model { file = "/net/cci-nas-00/data/ceres_data/8gv3_34282/06_2026/8gv3_34282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gv3_34282/06_2026/8gv3_34282.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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: 2.63, per 1000 atoms: 0.46 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: 0.52 Conformation dependent library (CDL) restraints added in 529.3 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: 0.21 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: 0.83 Time building geometry restraints manager: 0.68 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: 3136 17.69 - 35.38: 306 35.38 - 53.07: 76 53.07 - 70.75: 12 70.75 - 88.44: 16 Dihedral angle restraints: 3546 sinusoidal: 1448 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 3543 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: 0.360 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.420 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 15.901 88.441 2210 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 : 0.189 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: 0.0710 time to fit residues: 7.8383 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 : 0.250 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108193 restraints weight = 13920.230| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.33 r_work: 0.2954 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5850 Z= 0.122 Angle : 0.549 5.460 7930 Z= 0.277 Chirality : 0.046 0.127 908 Planarity : 0.004 0.037 992 Dihedral : 12.118 88.981 928 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.71 (0.30), residues: 744 helix: -0.22 (0.34), residues: 230 sheet: 0.42 (0.44), residues: 140 loop : -0.93 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.012 0.001 TYR A 179 PHE 0.005 0.001 PHE A 351 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 0.00291 / 0.12 ( 5836) covalent geometry : angle 0.53879 / 0.28 ( 7918) hydrogen bonds : bond 0.04078 / 2.78 ( 202) hydrogen bonds : angle 4.87135 / 3.43 ( 562) metal coordination : bond 0.00302 / 0.19 ( 14) metal coordination : angle 2.70656 / 1.83 ( 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 : 0.216 Fit side-chains REVERT: A 365 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7168 (tppt) REVERT: B 365 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7214 (tppt) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.0886 time to fit residues: 9.1494 Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 374 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105892 restraints weight = 8203.765| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.43 r_work: 0.2975 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5850 Z= 0.214 Angle : 0.609 5.744 7930 Z= 0.309 Chirality : 0.049 0.142 908 Planarity : 0.005 0.038 992 Dihedral : 12.145 89.972 928 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.83 % Allowed : 6.64 % Favored : 92.52 % 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: -0.88 (0.29), residues: 744 helix: -0.23 (0.34), residues: 230 sheet: 0.13 (0.43), residues: 140 loop : -1.03 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.015 0.002 TYR A 179 PHE 0.009 0.001 PHE A 197 TRP 0.027 0.003 TRP A 313 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.21 ( 5836) covalent geometry : angle 0.59586 / 0.31 ( 7918) hydrogen bonds : bond 0.05236 / 3.54 ( 202) hydrogen bonds : angle 4.78650 / 3.36 ( 562) metal coordination : bond 0.00650 / 0.41 ( 14) metal coordination : angle 3.31629 / 2.22 ( 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 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.219 Fit side-chains REVERT: A 365 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7236 (tppt) REVERT: B 365 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7244 (tppt) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.0865 time to fit residues: 8.0064 Evaluate side-chains 69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 313 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109119 restraints weight = 9798.327| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.70 r_work: 0.3010 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5850 Z= 0.097 Angle : 0.499 5.237 7930 Z= 0.251 Chirality : 0.045 0.125 908 Planarity : 0.004 0.036 992 Dihedral : 11.818 89.902 928 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.83 % Allowed : 7.31 % Favored : 91.86 % 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: -0.61 (0.30), residues: 744 helix: 0.16 (0.34), residues: 230 sheet: 0.19 (0.43), residues: 140 loop : -0.95 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.011 0.001 TYR A 179 PHE 0.003 0.001 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 0.00228 / 0.10 ( 5836) covalent geometry : angle 0.49054 / 0.25 ( 7918) hydrogen bonds : bond 0.03243 / 2.18 ( 202) hydrogen bonds : angle 4.41618 / 3.13 ( 562) metal coordination : bond 0.00226 / 0.13 ( 14) metal coordination : angle 2.39943 / 1.62 ( 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 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.195 Fit side-chains REVERT: A 365 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7191 (tppt) REVERT: B 365 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7224 (tppt) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.0819 time to fit residues: 7.9841 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106910 restraints weight = 14272.430| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.78 r_work: 0.2907 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5850 Z= 0.168 Angle : 0.554 5.632 7930 Z= 0.279 Chirality : 0.047 0.137 908 Planarity : 0.004 0.037 992 Dihedral : 11.830 89.939 928 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.33 % Allowed : 7.14 % Favored : 91.53 % 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: -0.68 (0.30), residues: 744 helix: 0.14 (0.35), residues: 230 sheet: 0.06 (0.43), residues: 140 loop : -0.98 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.012 0.001 TYR A 179 PHE 0.008 0.001 PHE B 197 TRP 0.026 0.002 TRP A 313 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 ( 5836) covalent geometry : angle 0.54222 / 0.28 ( 7918) hydrogen bonds : bond 0.04408 / 2.97 ( 202) hydrogen bonds : angle 4.51956 / 3.18 ( 562) metal coordination : bond 0.00514 / 0.32 ( 14) metal coordination : angle 2.93810 / 1.98 ( 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: 8 poor density : 65 time to evaluate : 0.326 Fit side-chains REVERT: A 365 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7185 (tppt) REVERT: B 365 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7192 (tppt) outliers start: 8 outliers final: 8 residues processed: 71 average time/residue: 0.0866 time to fit residues: 8.1253 Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106011 restraints weight = 13093.158| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.10 r_work: 0.2954 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1151 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= 0.153 Angle : 0.539 5.634 7930 Z= 0.272 Chirality : 0.047 0.134 908 Planarity : 0.004 0.038 992 Dihedral : 11.752 89.900 928 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.33 % Allowed : 8.14 % Favored : 90.53 % 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: -0.66 (0.30), residues: 744 helix: 0.21 (0.35), residues: 230 sheet: 0.05 (0.43), residues: 140 loop : -1.01 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.015 0.001 TYR B 179 PHE 0.006 0.001 PHE A 197 TRP 0.025 0.002 TRP B 313 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 ( 5836) covalent geometry : angle 0.52877 / 0.27 ( 7918) hydrogen bonds : bond 0.04116 / 2.77 ( 202) hydrogen bonds : angle 4.47601 / 3.15 ( 562) metal coordination : bond 0.00433 / 0.27 ( 14) metal coordination : angle 2.77022 / 1.86 ( 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: 8 poor density : 65 time to evaluate : 0.217 Fit side-chains REVERT: A 365 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7233 (tppt) REVERT: B 365 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7242 (tppt) outliers start: 8 outliers final: 8 residues processed: 71 average time/residue: 0.0829 time to fit residues: 7.6503 Evaluate side-chains 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 1.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106991 restraints weight = 17131.450| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.11 r_work: 0.2913 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1243 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= 0.116 Angle : 0.502 5.327 7930 Z= 0.252 Chirality : 0.046 0.130 908 Planarity : 0.004 0.037 992 Dihedral : 11.659 89.870 928 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.16 % Allowed : 9.47 % Favored : 89.37 % 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: -0.54 (0.30), residues: 744 helix: 0.36 (0.35), residues: 230 sheet: 0.10 (0.43), residues: 140 loop : -0.95 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.012 0.001 TYR B 179 PHE 0.004 0.001 PHE B 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 0.00286 / 0.12 ( 5836) covalent geometry : angle 0.49298 / 0.25 ( 7918) hydrogen bonds : bond 0.03492 / 2.34 ( 202) hydrogen bonds : angle 4.34781 / 3.07 ( 562) metal coordination : bond 0.00305 / 0.18 ( 14) metal coordination : angle 2.49564 / 1.68 ( 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 72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.264 Fit side-chains REVERT: A 365 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7192 (tppt) REVERT: B 365 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7165 (tppt) outliers start: 7 outliers final: 7 residues processed: 71 average time/residue: 0.0830 time to fit residues: 7.7767 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 : 0.159 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104567 restraints weight = 9784.203| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.74 r_work: 0.2958 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5850 Z= 0.189 Angle : 0.574 5.789 7930 Z= 0.289 Chirality : 0.048 0.140 908 Planarity : 0.004 0.039 992 Dihedral : 11.753 89.976 928 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.33 % Allowed : 9.97 % 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: -0.75 (0.30), residues: 744 helix: 0.22 (0.35), residues: 226 sheet: -0.07 (0.43), residues: 140 loop : -1.07 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.014 0.002 TYR B 179 PHE 0.009 0.001 PHE B 197 TRP 0.026 0.002 TRP B 313 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.19 ( 5836) covalent geometry : angle 0.56134 / 0.29 ( 7918) hydrogen bonds : bond 0.04681 / 3.16 ( 202) hydrogen bonds : angle 4.53495 / 3.18 ( 562) metal coordination : bond 0.00566 / 0.36 ( 14) metal coordination : angle 3.08612 / 2.05 ( 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 75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.208 Fit side-chains REVERT: A 160 ASP cc_start: 0.7201 (t0) cc_final: 0.6861 (t70) REVERT: A 365 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7243 (tppt) REVERT: B 365 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7247 (tppt) outliers start: 8 outliers final: 8 residues processed: 73 average time/residue: 0.0780 time to fit residues: 7.4904 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 : 0.220 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 33 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110789 restraints weight = 9413.890| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.58 r_work: 0.3034 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1411 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= 0.083 Angle : 0.475 5.108 7930 Z= 0.237 Chirality : 0.045 0.123 908 Planarity : 0.004 0.036 992 Dihedral : 11.524 89.615 928 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.33 % Allowed : 10.13 % Favored : 88.54 % 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: 0.49 (0.36), residues: 226 sheet: 0.10 (0.43), residues: 140 loop : -0.92 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 311 TYR 0.009 0.001 TYR A 179 PHE 0.003 0.001 PHE B 318 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 0.00185 / 0.08 ( 5836) covalent geometry : angle 0.46750 / 0.24 ( 7918) hydrogen bonds : bond 0.02827 / 1.90 ( 202) hydrogen bonds : angle 4.24225 / 3.01 ( 562) metal coordination : bond 0.00141 / 0.08 ( 14) metal coordination : angle 2.28060 / 1.51 ( 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 72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.228 Fit side-chains REVERT: A 365 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7182 (tppt) REVERT: B 365 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7223 (tppt) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.0870 time to fit residues: 7.9158 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 : 0.217 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.0670 chunk 66 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115550 restraints weight = 8123.191| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.47 r_work: 0.3087 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1722 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= 0.074 Angle : 0.452 4.665 7930 Z= 0.223 Chirality : 0.044 0.127 908 Planarity : 0.004 0.033 992 Dihedral : 11.299 89.288 928 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.00 % Allowed : 10.80 % Favored : 88.21 % 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: -0.20 (0.30), residues: 744 helix: 0.73 (0.37), residues: 226 sheet: 0.25 (0.44), residues: 140 loop : -0.79 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 128 TYR 0.006 0.001 TYR B 92 PHE 0.004 0.000 PHE A 318 TRP 0.021 0.002 TRP B 313 HIS 0.002 0.000 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00165 / 0.07 ( 5836) covalent geometry : angle 0.44319 / 0.22 ( 7918) hydrogen bonds : bond 0.02423 / 1.62 ( 202) hydrogen bonds : angle 4.01921 / 2.87 ( 562) metal coordination : bond 0.00191 / 0.10 ( 14) metal coordination : angle 2.35765 / 1.54 ( 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 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.141 Fit side-chains REVERT: A 237 THR cc_start: 0.8536 (m) cc_final: 0.8039 (p) REVERT: A 365 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7279 (tppt) REVERT: B 365 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7294 (tppt) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.0861 time to fit residues: 8.0700 Evaluate side-chains 69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.0370 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 72 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.149210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114008 restraints weight = 15047.250| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.53 r_work: 0.3011 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1696 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 : 0.453 4.578 7930 Z= 0.224 Chirality : 0.044 0.129 908 Planarity : 0.004 0.031 992 Dihedral : 11.220 89.271 928 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.66 % Allowed : 11.30 % Favored : 88.04 % 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: -0.12 (0.30), residues: 744 helix: 0.82 (0.37), residues: 226 sheet: 0.32 (0.44), residues: 140 loop : -0.76 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.008 0.001 TYR B 179 PHE 0.003 0.000 PHE A 318 TRP 0.021 0.002 TRP B 313 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.08 ( 5836) covalent geometry : angle 0.44501 / 0.22 ( 7918) hydrogen bonds : bond 0.02567 / 1.71 ( 202) hydrogen bonds : angle 4.03792 / 2.87 ( 562) metal coordination : bond 0.00184 / 0.10 ( 14) metal coordination : angle 2.24638 / 1.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.32 seconds wall clock time: 27 minutes 37.71 seconds (1657.71 seconds total)