Starting phenix.real_space_refine on Wed Jan 15 16:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map" model { file = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2770 2.51 5 N 725 2.21 5 O 900 1.98 5 H 4190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 4.12, per 1000 atoms: 0.48 Number of scatterers: 8595 At special positions: 0 Unit cell: (91.567, 114.681, 44.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 900 8.00 N 725 7.00 C 2770 6.00 H 4190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.04 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 Links applied NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 700.2 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.295A pdb=" N GLU B 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.378A pdb=" N SER B 9 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL D 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER A 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER A 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.872A pdb=" N THR B 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D 20 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN B 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS D 22 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 21 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N CYS B 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A 21 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 18 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR C 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N SER C 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 22 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.181A pdb=" N TYR B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU D 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 28 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 37 removed outlier: 6.266A pdb=" N SER B 33 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN D 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR B 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER A 33 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 36 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52 removed outlier: 6.787A pdb=" N VAL B 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ILE D 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLN D 49 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR B 48 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N SER D 51 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 50 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.507A pdb=" N THR B 73 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86 removed outlier: 6.879A pdb=" N ALA B 83 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE D 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 85 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 97 removed outlier: 7.095A pdb=" N PHE B 97 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 97 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR C 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 92 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL C 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE C 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A 96 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR E 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE C 92 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL E 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE E 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL C 96 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 102 through 103 removed outlier: 6.183A pdb=" N LYS B 102 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 102 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 116 removed outlier: 6.315A pdb=" N VAL A 115 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 115 " --> pdb=" O THR E 116 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4190 1.04 - 1.24: 655 1.24 - 1.45: 1368 1.45 - 1.65: 2482 1.65 - 1.86: 10 Bond restraints: 8705 Sorted by residual: bond pdb=" CA THR A 21 " pdb=" C THR A 21 " ideal model delta sigma weight residual 1.521 1.542 -0.021 1.26e-02 6.30e+03 2.70e+00 bond pdb=" CA THR B 21 " pdb=" C THR B 21 " ideal model delta sigma weight residual 1.521 1.541 -0.021 1.26e-02 6.30e+03 2.65e+00 bond pdb=" CA THR C 21 " pdb=" C THR C 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.61e+00 bond pdb=" CA THR D 21 " pdb=" C THR D 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.60e+00 bond pdb=" CA THR E 21 " pdb=" C THR E 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.56e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14274 1.95 - 3.89: 1141 3.89 - 5.84: 185 5.84 - 7.78: 40 7.78 - 9.73: 10 Bond angle restraints: 15650 Sorted by residual: angle pdb=" N THR B 77 " pdb=" CA THR B 77 " pdb=" C THR B 77 " ideal model delta sigma weight residual 111.07 116.38 -5.31 1.07e+00 8.73e-01 2.46e+01 angle pdb=" N THR A 77 " pdb=" CA THR A 77 " pdb=" C THR A 77 " ideal model delta sigma weight residual 111.07 116.35 -5.28 1.07e+00 8.73e-01 2.44e+01 angle pdb=" N THR C 77 " pdb=" CA THR C 77 " pdb=" C THR C 77 " ideal model delta sigma weight residual 111.07 116.34 -5.27 1.07e+00 8.73e-01 2.43e+01 angle pdb=" N THR E 77 " pdb=" CA THR E 77 " pdb=" C THR E 77 " ideal model delta sigma weight residual 111.07 116.31 -5.24 1.07e+00 8.73e-01 2.40e+01 angle pdb=" N THR D 77 " pdb=" CA THR D 77 " pdb=" C THR D 77 " ideal model delta sigma weight residual 111.07 116.30 -5.23 1.07e+00 8.73e-01 2.39e+01 ... (remaining 15645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 3759 14.68 - 29.37: 309 29.37 - 44.05: 90 44.05 - 58.73: 95 58.73 - 73.42: 30 Dihedral angle restraints: 4283 sinusoidal: 2363 harmonic: 1920 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N ALA A 70 " pdb=" CA ALA A 70 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR C 69 " pdb=" C THR C 69 " pdb=" N ALA C 70 " pdb=" CA ALA C 70 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR D 69 " pdb=" C THR D 69 " pdb=" N ALA D 70 " pdb=" CA ALA D 70 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 309 0.038 - 0.076: 209 0.076 - 0.113: 94 0.113 - 0.151: 58 0.151 - 0.189: 30 Chirality restraints: 700 Sorted by residual: chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" C1 NAG C 201 " pdb=" ND2 ASN C 19 " pdb=" C2 NAG C 201 " pdb=" O5 NAG C 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 697 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 90 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.27e+01 pdb=" CG TRP E 90 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP E 90 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 90 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP E 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP E 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 90 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TRP E 90 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP E 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP E 90 " 0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 90 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 90 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.26e+01 pdb=" CG TRP C 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 90 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 90 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP C 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 90 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP C 90 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP C 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP C 90 " 0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 90 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 90 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 90 " -0.005 2.00e-02 2.50e+03 1.77e-02 1.26e+01 pdb=" CG TRP D 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 90 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 90 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP D 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP D 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP D 90 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP D 90 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP D 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP D 90 " 0.010 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 90 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP D 90 " -0.020 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 3589 2.38 - 2.93: 18474 2.93 - 3.49: 19251 3.49 - 4.04: 28985 4.04 - 4.60: 40178 Nonbonded interactions: 110477 Sorted by model distance: nonbonded pdb=" O THR B 104 " pdb=" HG1 THR B 104 " model vdw 1.824 2.450 nonbonded pdb=" O THR D 104 " pdb=" HG1 THR D 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR A 104 " pdb=" HG1 THR A 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR C 104 " pdb=" HG1 THR C 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR E 104 " pdb=" HG1 THR E 104 " model vdw 1.825 2.450 ... (remaining 110472 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.790 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: 0.160 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 0.010 0.058 4515 Z= 0.690 Angle : 1.566 9.728 6160 Z= 0.923 Chirality : 0.070 0.189 700 Planarity : 0.007 0.051 795 Dihedral : 11.241 73.418 1675 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.009 TRP A 90 PHE 0.022 0.005 PHE A 2 TYR 0.040 0.008 TYR B 85 ARG 0.005 0.002 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8487 (mt) cc_final: 0.8181 (mt) REVERT: A 78 GLN cc_start: 0.7987 (tt0) cc_final: 0.7777 (tt0) REVERT: A 110 LYS cc_start: 0.7916 (tptm) cc_final: 0.7643 (mptt) REVERT: A 115 VAL cc_start: 0.6206 (t) cc_final: 0.5965 (t) REVERT: C 88 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 110 LYS cc_start: 0.8031 (tptm) cc_final: 0.7584 (mptt) REVERT: D 38 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8316 (mmtt) REVERT: D 78 GLN cc_start: 0.8016 (tt0) cc_final: 0.7484 (tp-100) REVERT: E 36 GLN cc_start: 0.7393 (tt0) cc_final: 0.7024 (pm20) REVERT: E 61 PHE cc_start: 0.5374 (p90) cc_final: 0.5058 (t80) REVERT: E 72 LEU cc_start: 0.8601 (tp) cc_final: 0.8397 (pp) REVERT: E 86 PHE cc_start: 0.6696 (m-80) cc_final: 0.6025 (p90) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3081 time to fit residues: 53.7184 Evaluate side-chains 66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.152843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.135601 restraints weight = 25661.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.139872 restraints weight = 11443.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.142495 restraints weight = 6338.987| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4515 Z= 0.269 Angle : 0.721 4.946 6160 Z= 0.389 Chirality : 0.049 0.217 700 Planarity : 0.005 0.040 795 Dihedral : 6.109 19.381 725 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.68 % Allowed : 9.07 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 34 PHE 0.017 0.002 PHE C 2 TYR 0.029 0.003 TYR A 31 ARG 0.004 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7938 (tptm) cc_final: 0.7597 (mptt) REVERT: C 110 LYS cc_start: 0.7982 (tptm) cc_final: 0.7529 (mptt) REVERT: D 38 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8003 (mmtt) REVERT: E 36 GLN cc_start: 0.7838 (tt0) cc_final: 0.7586 (pm20) REVERT: E 86 PHE cc_start: 0.6503 (m-80) cc_final: 0.5774 (p90) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.2708 time to fit residues: 32.1013 Evaluate side-chains 65 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 88 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 68 ASN A 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.151117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.134056 restraints weight = 26081.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.138186 restraints weight = 12005.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.140769 restraints weight = 6773.151| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4515 Z= 0.242 Angle : 0.630 4.099 6160 Z= 0.335 Chirality : 0.047 0.205 700 Planarity : 0.005 0.042 795 Dihedral : 6.107 27.266 725 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.27 % Allowed : 11.13 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.21), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.16), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 90 PHE 0.011 0.001 PHE A 2 TYR 0.014 0.002 TYR A 31 ARG 0.002 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7861 (tptm) cc_final: 0.7561 (mptt) REVERT: C 110 LYS cc_start: 0.7926 (tptm) cc_final: 0.7569 (mptt) REVERT: D 38 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8172 (mmtt) REVERT: E 86 PHE cc_start: 0.6226 (m-80) cc_final: 0.5598 (p90) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.2912 time to fit residues: 25.6464 Evaluate side-chains 64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 88 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.134821 restraints weight = 25634.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.138971 restraints weight = 11894.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.141600 restraints weight = 6646.694| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4515 Z= 0.208 Angle : 0.575 3.844 6160 Z= 0.303 Chirality : 0.046 0.180 700 Planarity : 0.005 0.042 795 Dihedral : 6.218 30.887 725 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.47 % Allowed : 11.34 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 90 PHE 0.011 0.001 PHE B 61 TYR 0.010 0.002 TYR C 85 ARG 0.001 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7833 (tptm) cc_final: 0.7567 (mptt) REVERT: C 110 LYS cc_start: 0.7934 (tptm) cc_final: 0.7520 (mptt) REVERT: D 38 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8047 (mmtt) REVERT: E 86 PHE cc_start: 0.6254 (m-80) cc_final: 0.5641 (p90) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.2817 time to fit residues: 24.8798 Evaluate side-chains 64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN D 41 GLN D 68 ASN E 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.150776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.133459 restraints weight = 25407.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.137763 restraints weight = 11447.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.140434 restraints weight = 6334.651| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4515 Z= 0.244 Angle : 0.589 5.584 6160 Z= 0.311 Chirality : 0.047 0.183 700 Planarity : 0.005 0.044 795 Dihedral : 6.776 37.915 725 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.27 % Allowed : 11.55 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 90 PHE 0.009 0.001 PHE B 61 TYR 0.013 0.002 TYR A 85 ARG 0.002 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.624 Fit side-chains REVERT: C 110 LYS cc_start: 0.7943 (tptm) cc_final: 0.7595 (mptt) REVERT: D 38 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8149 (mmtt) REVERT: E 86 PHE cc_start: 0.6332 (m-80) cc_final: 0.5482 (p90) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.3085 time to fit residues: 26.0070 Evaluate side-chains 61 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0470 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.151647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.134925 restraints weight = 25262.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.139074 restraints weight = 11556.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.141637 restraints weight = 6455.815| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4515 Z= 0.170 Angle : 0.533 4.816 6160 Z= 0.276 Chirality : 0.046 0.159 700 Planarity : 0.005 0.042 795 Dihedral : 5.959 30.181 725 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.86 % Allowed : 12.99 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 90 PHE 0.007 0.001 PHE B 61 TYR 0.008 0.001 TYR A 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.608 Fit side-chains REVERT: C 110 LYS cc_start: 0.8063 (tptm) cc_final: 0.7657 (mptt) REVERT: D 38 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8111 (mmtt) REVERT: E 86 PHE cc_start: 0.6316 (m-80) cc_final: 0.5550 (p90) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.3051 time to fit residues: 25.0945 Evaluate side-chains 61 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.134834 restraints weight = 25471.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.139215 restraints weight = 11453.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.141933 restraints weight = 6337.020| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4515 Z= 0.179 Angle : 0.530 3.971 6160 Z= 0.275 Chirality : 0.045 0.152 700 Planarity : 0.005 0.042 795 Dihedral : 6.013 32.163 725 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.65 % Allowed : 13.81 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 PHE 0.013 0.001 PHE C 86 TYR 0.009 0.001 TYR A 85 ARG 0.001 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.649 Fit side-chains REVERT: C 110 LYS cc_start: 0.8051 (tptm) cc_final: 0.7648 (mptt) REVERT: D 38 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8142 (mmtt) REVERT: E 86 PHE cc_start: 0.6425 (m-80) cc_final: 0.5537 (p90) outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.3169 time to fit residues: 24.4371 Evaluate side-chains 59 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.152332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.135368 restraints weight = 25092.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.139623 restraints weight = 11309.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.142238 restraints weight = 6259.434| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4515 Z= 0.185 Angle : 0.530 3.903 6160 Z= 0.275 Chirality : 0.045 0.152 700 Planarity : 0.005 0.042 795 Dihedral : 6.126 33.538 725 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.47 % Allowed : 12.78 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 90 PHE 0.013 0.001 PHE C 86 TYR 0.009 0.001 TYR A 85 ARG 0.002 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.643 Fit side-chains REVERT: C 110 LYS cc_start: 0.8070 (tptm) cc_final: 0.7698 (mptt) REVERT: D 38 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8168 (mmtt) REVERT: E 86 PHE cc_start: 0.6420 (m-80) cc_final: 0.5543 (p90) outliers start: 12 outliers final: 12 residues processed: 59 average time/residue: 0.2937 time to fit residues: 22.8169 Evaluate side-chains 63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.153764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.136588 restraints weight = 25480.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.140996 restraints weight = 11505.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.143727 restraints weight = 6388.097| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4515 Z= 0.139 Angle : 0.495 3.890 6160 Z= 0.253 Chirality : 0.045 0.140 700 Planarity : 0.005 0.040 795 Dihedral : 5.375 26.802 725 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.06 % Allowed : 12.58 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 PHE 0.014 0.001 PHE C 86 TYR 0.006 0.001 TYR A 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.623 Fit side-chains REVERT: C 110 LYS cc_start: 0.8085 (tptm) cc_final: 0.7702 (mptt) REVERT: D 38 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8164 (mmtt) REVERT: E 86 PHE cc_start: 0.6345 (m-80) cc_final: 0.5487 (p90) outliers start: 10 outliers final: 10 residues processed: 59 average time/residue: 0.3124 time to fit residues: 24.3133 Evaluate side-chains 63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.152284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.135421 restraints weight = 25274.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.139683 restraints weight = 11401.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.142290 restraints weight = 6314.481| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4515 Z= 0.185 Angle : 0.526 4.333 6160 Z= 0.272 Chirality : 0.045 0.151 700 Planarity : 0.005 0.042 795 Dihedral : 5.895 32.442 725 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.27 % Allowed : 12.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 90 PHE 0.013 0.001 PHE C 86 TYR 0.011 0.001 TYR A 85 ARG 0.002 0.000 ARG D 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.709 Fit side-chains REVERT: C 110 LYS cc_start: 0.8107 (tptm) cc_final: 0.7729 (mptt) REVERT: D 38 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8171 (mmtt) REVERT: E 86 PHE cc_start: 0.6397 (m-80) cc_final: 0.5480 (p90) outliers start: 11 outliers final: 11 residues processed: 56 average time/residue: 0.3049 time to fit residues: 22.6036 Evaluate side-chains 62 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.154124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.137457 restraints weight = 25498.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.141679 restraints weight = 11767.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.144311 restraints weight = 6582.415| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4515 Z= 0.143 Angle : 0.498 3.890 6160 Z= 0.254 Chirality : 0.045 0.142 700 Planarity : 0.004 0.039 795 Dihedral : 5.374 27.770 725 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.27 % Allowed : 12.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 90 PHE 0.012 0.001 PHE C 86 TYR 0.006 0.001 TYR A 85 ARG 0.001 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.02 seconds wall clock time: 57 minutes 29.24 seconds (3449.24 seconds total)