Starting phenix.real_space_refine on Mon Aug 25 16:26:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.map" model { file = "/net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kay_62216/08_2025/9kay_62216.cif" } resolution = 1.73 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 18936 2.51 5 N 5496 2.21 5 O 5592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30168 Number of models: 1 Model: "" Number of chains: 24 Chain: "Aa" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ab" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ac" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ad" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ae" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Af" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ag" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ah" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ai" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Aj" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ak" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Al" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Am" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "An" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ao" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ap" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Aq" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ar" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "As" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "At" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Au" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Av" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Aw" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Ax" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Time building chain proxies: 6.08, per 1000 atoms: 0.20 Number of scatterers: 30168 At special positions: 0 Unit cell: (126.67, 126.67, 126.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5592 8.00 N 5496 7.00 C 18936 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'Aa' and resid 13 through 42 Processing helix chain 'Aa' and resid 48 through 76 Processing helix chain 'Aa' and resid 95 through 124 Processing helix chain 'Aa' and resid 126 through 137 Processing helix chain 'Aa' and resid 137 through 156 Processing helix chain 'Ab' and resid 13 through 42 Processing helix chain 'Ab' and resid 48 through 76 Processing helix chain 'Ab' and resid 95 through 124 Processing helix chain 'Ab' and resid 126 through 137 Processing helix chain 'Ab' and resid 137 through 156 Processing helix chain 'Ac' and resid 13 through 41 Processing helix chain 'Ac' and resid 48 through 76 Processing helix chain 'Ac' and resid 95 through 124 Processing helix chain 'Ac' and resid 126 through 137 Processing helix chain 'Ac' and resid 137 through 156 Processing helix chain 'Ad' and resid 13 through 41 Processing helix chain 'Ad' and resid 48 through 76 Processing helix chain 'Ad' and resid 95 through 124 Processing helix chain 'Ad' and resid 126 through 137 Processing helix chain 'Ad' and resid 137 through 156 Processing helix chain 'Ae' and resid 13 through 42 Processing helix chain 'Ae' and resid 48 through 76 Processing helix chain 'Ae' and resid 95 through 124 Processing helix chain 'Ae' and resid 126 through 137 Processing helix chain 'Ae' and resid 137 through 156 Processing helix chain 'Af' and resid 13 through 42 Processing helix chain 'Af' and resid 48 through 76 Processing helix chain 'Af' and resid 95 through 124 Processing helix chain 'Af' and resid 126 through 137 Processing helix chain 'Af' and resid 137 through 156 Processing helix chain 'Ag' and resid 13 through 41 Processing helix chain 'Ag' and resid 48 through 76 Processing helix chain 'Ag' and resid 95 through 124 Processing helix chain 'Ag' and resid 126 through 137 Processing helix chain 'Ag' and resid 137 through 156 Processing helix chain 'Ah' and resid 13 through 42 Processing helix chain 'Ah' and resid 48 through 76 Processing helix chain 'Ah' and resid 95 through 124 Processing helix chain 'Ah' and resid 126 through 137 Processing helix chain 'Ah' and resid 137 through 156 Processing helix chain 'Ai' and resid 13 through 42 Processing helix chain 'Ai' and resid 48 through 76 Processing helix chain 'Ai' and resid 95 through 124 Processing helix chain 'Ai' and resid 126 through 137 Processing helix chain 'Ai' and resid 137 through 156 Processing helix chain 'Aj' and resid 13 through 41 Processing helix chain 'Aj' and resid 48 through 76 Processing helix chain 'Aj' and resid 95 through 124 Processing helix chain 'Aj' and resid 126 through 137 Processing helix chain 'Aj' and resid 137 through 156 Processing helix chain 'Ak' and resid 13 through 41 Processing helix chain 'Ak' and resid 48 through 76 Processing helix chain 'Ak' and resid 95 through 124 Processing helix chain 'Ak' and resid 126 through 137 Processing helix chain 'Ak' and resid 137 through 156 Processing helix chain 'Al' and resid 13 through 41 Processing helix chain 'Al' and resid 48 through 76 Processing helix chain 'Al' and resid 95 through 124 Processing helix chain 'Al' and resid 126 through 137 Processing helix chain 'Al' and resid 137 through 156 Processing helix chain 'Am' and resid 13 through 41 Processing helix chain 'Am' and resid 48 through 76 Processing helix chain 'Am' and resid 95 through 124 Processing helix chain 'Am' and resid 126 through 137 Processing helix chain 'Am' and resid 137 through 156 Processing helix chain 'An' and resid 13 through 42 Processing helix chain 'An' and resid 48 through 76 Processing helix chain 'An' and resid 95 through 124 Processing helix chain 'An' and resid 126 through 137 Processing helix chain 'An' and resid 137 through 156 Processing helix chain 'Ao' and resid 13 through 42 Processing helix chain 'Ao' and resid 48 through 76 Processing helix chain 'Ao' and resid 95 through 124 Processing helix chain 'Ao' and resid 126 through 137 Processing helix chain 'Ao' and resid 137 through 156 Processing helix chain 'Ap' and resid 13 through 42 Processing helix chain 'Ap' and resid 48 through 76 Processing helix chain 'Ap' and resid 95 through 124 Processing helix chain 'Ap' and resid 126 through 137 Processing helix chain 'Ap' and resid 137 through 156 Processing helix chain 'Aq' and resid 13 through 42 Processing helix chain 'Aq' and resid 48 through 76 Processing helix chain 'Aq' and resid 95 through 124 Processing helix chain 'Aq' and resid 126 through 137 Processing helix chain 'Aq' and resid 137 through 156 Processing helix chain 'Ar' and resid 13 through 41 Processing helix chain 'Ar' and resid 48 through 76 Processing helix chain 'Ar' and resid 95 through 124 Processing helix chain 'Ar' and resid 126 through 137 Processing helix chain 'Ar' and resid 137 through 156 Processing helix chain 'As' and resid 13 through 42 Processing helix chain 'As' and resid 48 through 76 Processing helix chain 'As' and resid 95 through 124 Processing helix chain 'As' and resid 126 through 137 Processing helix chain 'As' and resid 137 through 156 Processing helix chain 'At' and resid 13 through 42 Processing helix chain 'At' and resid 48 through 76 Processing helix chain 'At' and resid 95 through 124 Processing helix chain 'At' and resid 126 through 137 Processing helix chain 'At' and resid 137 through 156 Processing helix chain 'Au' and resid 13 through 42 Processing helix chain 'Au' and resid 48 through 76 Processing helix chain 'Au' and resid 95 through 124 Processing helix chain 'Au' and resid 126 through 137 Processing helix chain 'Au' and resid 137 through 156 Processing helix chain 'Av' and resid 13 through 41 Processing helix chain 'Av' and resid 48 through 76 Processing helix chain 'Av' and resid 95 through 124 Processing helix chain 'Av' and resid 126 through 137 Processing helix chain 'Av' and resid 137 through 156 Processing helix chain 'Aw' and resid 13 through 42 Processing helix chain 'Aw' and resid 48 through 76 Processing helix chain 'Aw' and resid 95 through 124 Processing helix chain 'Aw' and resid 126 through 137 Processing helix chain 'Aw' and resid 137 through 156 Processing helix chain 'Ax' and resid 13 through 42 Processing helix chain 'Ax' and resid 48 through 76 Processing helix chain 'Ax' and resid 95 through 124 Processing helix chain 'Ax' and resid 126 through 137 Processing helix chain 'Ax' and resid 137 through 156 2415 hydrogen bonds defined for protein. 7245 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: 4.64 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10248 1.34 - 1.46: 4092 1.46 - 1.58: 16212 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 30768 Sorted by residual: bond pdb=" N ASPAx 84 " pdb=" CA ASPAx 84 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.67e+00 bond pdb=" N ILEAx 85 " pdb=" CA ILEAx 85 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.15e-02 7.56e+03 7.16e+00 bond pdb=" N ASPAx 91 " pdb=" CA ASPAx 91 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.28e-02 6.10e+03 6.78e+00 bond pdb=" N CYSAx 90 " pdb=" CA CYSAx 90 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" N ASPAx 92 " pdb=" CA ASPAx 92 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.27e-02 6.20e+03 6.02e+00 ... (remaining 30763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 39801 1.35 - 2.70: 1266 2.70 - 4.06: 154 4.06 - 5.41: 108 5.41 - 6.76: 23 Bond angle restraints: 41352 Sorted by residual: angle pdb=" CA ASPAx 84 " pdb=" CB ASPAx 84 " pdb=" CG ASPAx 84 " ideal model delta sigma weight residual 112.60 116.44 -3.84 1.00e+00 1.00e+00 1.48e+01 angle pdb=" N GLUAw 94 " pdb=" CA GLUAw 94 " pdb=" C GLUAw 94 " ideal model delta sigma weight residual 110.80 117.56 -6.76 2.13e+00 2.20e-01 1.01e+01 angle pdb=" N GLUAl 94 " pdb=" CA GLUAl 94 " pdb=" C GLUAl 94 " ideal model delta sigma weight residual 110.80 117.55 -6.75 2.13e+00 2.20e-01 1.00e+01 angle pdb=" N GLUAv 94 " pdb=" CA GLUAv 94 " pdb=" C GLUAv 94 " ideal model delta sigma weight residual 110.80 117.52 -6.72 2.13e+00 2.20e-01 9.97e+00 angle pdb=" N GLUAn 94 " pdb=" CA GLUAn 94 " pdb=" C GLUAn 94 " ideal model delta sigma weight residual 110.80 117.47 -6.67 2.13e+00 2.20e-01 9.81e+00 ... (remaining 41347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 17060 17.33 - 34.66: 1304 34.66 - 51.99: 275 51.99 - 69.32: 68 69.32 - 86.64: 61 Dihedral angle restraints: 18768 sinusoidal: 7920 harmonic: 10848 Sorted by residual: dihedral pdb=" CA TRPAa 93 " pdb=" C TRPAa 93 " pdb=" N GLUAa 94 " pdb=" CA GLUAa 94 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA TRPAi 93 " pdb=" C TRPAi 93 " pdb=" N GLUAi 94 " pdb=" CA GLUAi 94 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TRPAo 93 " pdb=" C TRPAo 93 " pdb=" N GLUAo 94 " pdb=" CA GLUAo 94 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 18765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3345 0.039 - 0.079: 731 0.079 - 0.118: 196 0.118 - 0.157: 71 0.157 - 0.197: 1 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CA ILEAx 85 " pdb=" N ILEAx 85 " pdb=" C ILEAx 85 " pdb=" CB ILEAx 85 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA TYRAn 39 " pdb=" N TYRAn 39 " pdb=" C TYRAn 39 " pdb=" CB TYRAn 39 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYRAb 39 " pdb=" N TYRAb 39 " pdb=" C TYRAb 39 " pdb=" CB TYRAb 39 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 4341 not shown) Planarity restraints: 5400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRAc 39 " 0.016 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYRAc 39 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYRAc 39 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYRAc 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYRAc 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYRAc 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYRAc 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYRAc 39 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAi 39 " -0.015 2.00e-02 2.50e+03 9.76e-03 1.91e+00 pdb=" CG TYRAi 39 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYRAi 39 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYRAi 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYRAi 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRAi 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYRAi 39 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRAi 39 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPAm 93 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C TRPAm 93 " 0.024 2.00e-02 2.50e+03 pdb=" O TRPAm 93 " -0.009 2.00e-02 2.50e+03 pdb=" N GLUAm 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 5397 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7786 2.83 - 3.34: 31124 3.34 - 3.86: 54283 3.86 - 4.38: 62891 4.38 - 4.90: 102368 Nonbonded interactions: 258452 Sorted by model distance: nonbonded pdb=" OH TYRAr 54 " pdb=" NZ LYSAr 147 " model vdw 2.308 3.120 nonbonded pdb=" OH TYRAv 54 " pdb=" NZ LYSAv 147 " model vdw 2.364 3.120 nonbonded pdb=" OH TYRAo 54 " pdb=" NZ LYSAo 147 " model vdw 2.367 3.120 nonbonded pdb=" OH TYRAf 54 " pdb=" NZ LYSAf 147 " model vdw 2.380 3.120 nonbonded pdb=" OH TYRAw 54 " pdb=" NZ LYSAw 147 " model vdw 2.382 3.120 ... (remaining 258447 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 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.040 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30768 Z= 0.190 Angle : 0.626 6.760 41352 Z= 0.379 Chirality : 0.039 0.197 4344 Planarity : 0.003 0.029 5400 Dihedral : 14.130 86.644 11712 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.22 (0.14), residues: 3576 helix: 4.11 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : 0.03 (0.29), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAk 76 TYR 0.025 0.003 TYRAc 39 PHE 0.018 0.002 PHEAx 41 TRP 0.013 0.001 TRPAv 93 HIS 0.005 0.001 HISAk 105 Details of bonding type rmsd covalent geometry : bond 0.00320 (30768) covalent geometry : angle 0.62622 (41352) hydrogen bonds : bond 0.10087 ( 2415) hydrogen bonds : angle 4.00804 ( 7245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 545 time to evaluate : 1.386 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 547 average time/residue: 1.0456 time to fit residues: 632.1976 Evaluate side-chains 534 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 14 GLN Ab 14 GLN Ad 14 GLN Ae 14 GLN Af 14 GLN Ag 14 GLN Ah 14 GLN Ai 14 GLN Aj 14 GLN Aj 139 ASN Ak 14 GLN Al 14 GLN Am 14 GLN An 14 GLN Ao 14 GLN Ap 14 GLN Aq 14 GLN Ar 14 GLN As 14 GLN At 14 GLN Au 14 GLN Av 14 GLN Aw 14 GLN Ax 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126447 restraints weight = 18977.030| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.31 r_work: 0.3338 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3095 rms_B_bonded: 3.00 restraints_weight: 0.1250 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30768 Z= 0.184 Angle : 0.593 7.415 41352 Z= 0.329 Chirality : 0.038 0.156 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.102 21.727 3984 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.82 % Allowed : 5.14 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.07 (0.14), residues: 3576 helix: 3.95 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.10 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAx 63 TYR 0.024 0.003 TYRAg 39 PHE 0.019 0.002 PHEAg 41 TRP 0.010 0.001 TRPAn 93 HIS 0.005 0.001 HISAt 128 Details of bonding type rmsd covalent geometry : bond 0.00322 (30768) covalent geometry : angle 0.59308 (41352) hydrogen bonds : bond 0.08702 ( 2415) hydrogen bonds : angle 3.85064 ( 7245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 561 time to evaluate : 1.331 Fit side-chains outliers start: 27 outliers final: 0 residues processed: 568 average time/residue: 1.1719 time to fit residues: 735.4451 Evaluate side-chains 539 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 229 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.135299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129949 restraints weight = 19118.178| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.32 r_work: 0.3382 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3139 rms_B_bonded: 3.04 restraints_weight: 0.1250 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 30768 Z= 0.150 Angle : 0.521 6.426 41352 Z= 0.287 Chirality : 0.036 0.150 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.986 21.660 3984 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.82 % Allowed : 5.78 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.48 (0.14), residues: 3576 helix: 4.25 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAu 9 TYR 0.019 0.002 TYRAs 39 PHE 0.013 0.001 PHEAl 41 TRP 0.008 0.001 TRPAv 93 HIS 0.003 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00246 (30768) covalent geometry : angle 0.52140 (41352) hydrogen bonds : bond 0.07446 ( 2415) hydrogen bonds : angle 3.64167 ( 7245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 545 time to evaluate : 1.373 Fit side-chains REVERT: Av 94 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7897 (mm-30) REVERT: Aw 94 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7897 (mm-30) outliers start: 27 outliers final: 0 residues processed: 549 average time/residue: 1.1705 time to fit residues: 710.1572 Evaluate side-chains 537 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 213 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 336 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 292 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.133920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126508 restraints weight = 19269.695| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.51 r_work: 0.3338 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3086 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30768 Z= 0.163 Angle : 0.549 6.815 41352 Z= 0.302 Chirality : 0.037 0.150 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.978 22.216 3984 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.85 % Allowed : 5.50 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.35 (0.14), residues: 3576 helix: 4.16 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAx 63 TYR 0.020 0.002 TYRAc 39 PHE 0.015 0.002 PHEAg 41 TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00276 (30768) covalent geometry : angle 0.54881 (41352) hydrogen bonds : bond 0.07989 ( 2415) hydrogen bonds : angle 3.72670 ( 7245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 538 time to evaluate : 1.069 Fit side-chains REVERT: Av 94 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7481 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7560 (mm-30) outliers start: 28 outliers final: 0 residues processed: 542 average time/residue: 0.9925 time to fit residues: 594.8675 Evaluate side-chains 538 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 164 optimal weight: 0.3980 chunk 310 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 307 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.139478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131679 restraints weight = 19644.383| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.56 r_work: 0.3400 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.3151 rms_B_bonded: 3.78 restraints_weight: 0.1250 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 30768 Z= 0.133 Angle : 0.491 6.628 41352 Z= 0.267 Chirality : 0.035 0.144 4344 Planarity : 0.002 0.026 5400 Dihedral : 3.882 21.872 3984 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.82 % Allowed : 5.38 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.83 (0.14), residues: 3576 helix: 4.50 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.26 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAr 64 TYR 0.016 0.002 TYRAu 39 PHE 0.009 0.001 PHEAv 41 TRP 0.008 0.001 TRPAl 93 HIS 0.003 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00220 (30768) covalent geometry : angle 0.49128 (41352) hydrogen bonds : bond 0.06351 ( 2415) hydrogen bonds : angle 3.42816 ( 7245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 541 time to evaluate : 1.086 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7258 (mm-30) REVERT: Av 94 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7229 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7316 (mm-30) outliers start: 27 outliers final: 0 residues processed: 545 average time/residue: 0.9649 time to fit residues: 582.3195 Evaluate side-chains 546 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 546 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 230 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.133015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125632 restraints weight = 19271.855| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 0.50 r_work: 0.3326 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3074 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30768 Z= 0.176 Angle : 0.575 7.141 41352 Z= 0.316 Chirality : 0.037 0.147 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.951 22.105 3984 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.43 % Allowed : 6.14 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.35 (0.14), residues: 3576 helix: 4.14 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.21 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAx 63 TYR 0.022 0.003 TYRAc 39 PHE 0.018 0.002 PHEAx 41 TRP 0.009 0.001 TRPAn 93 HIS 0.005 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00311 (30768) covalent geometry : angle 0.57519 (41352) hydrogen bonds : bond 0.08335 ( 2415) hydrogen bonds : angle 3.76115 ( 7245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 537 time to evaluate : 0.940 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7519 (mm-30) REVERT: Av 94 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7504 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7585 (mm-30) outliers start: 14 outliers final: 0 residues processed: 541 average time/residue: 0.9571 time to fit residues: 572.5129 Evaluate side-chains 538 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 241 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 356 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 341 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.134372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127051 restraints weight = 19315.286| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.50 r_work: 0.3345 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work: 0.3093 rms_B_bonded: 3.51 restraints_weight: 0.1250 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30768 Z= 0.162 Angle : 0.552 6.631 41352 Z= 0.302 Chirality : 0.036 0.149 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.965 22.325 3984 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.82 % Allowed : 5.75 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.42 (0.14), residues: 3576 helix: 4.20 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAx 63 TYR 0.020 0.002 TYRAp 39 PHE 0.015 0.002 PHEAg 41 TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00281 (30768) covalent geometry : angle 0.55161 (41352) hydrogen bonds : bond 0.07809 ( 2415) hydrogen bonds : angle 3.69787 ( 7245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 539 time to evaluate : 1.182 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7487 (mm-30) REVERT: Av 94 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7475 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7547 (mm-30) outliers start: 27 outliers final: 0 residues processed: 543 average time/residue: 0.9445 time to fit residues: 567.4978 Evaluate side-chains 537 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 87 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.134753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127431 restraints weight = 19328.940| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.51 r_work: 0.3350 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.1250 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30768 Z= 0.159 Angle : 0.552 6.605 41352 Z= 0.300 Chirality : 0.036 0.148 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.942 22.271 3984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.18 % Allowed : 6.78 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.47 (0.14), residues: 3576 helix: 4.23 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.21 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAx 63 TYR 0.019 0.002 TYRAp 39 PHE 0.014 0.001 PHEAg 41 TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00275 (30768) covalent geometry : angle 0.55210 (41352) hydrogen bonds : bond 0.07654 ( 2415) hydrogen bonds : angle 3.67311 ( 7245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 538 time to evaluate : 0.978 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7487 (mm-30) REVERT: Av 94 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7477 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7543 (mm-30) outliers start: 6 outliers final: 0 residues processed: 542 average time/residue: 0.9743 time to fit residues: 582.8410 Evaluate side-chains 537 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 127 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125407 restraints weight = 19170.005| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.50 r_work: 0.3325 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work: 0.3073 rms_B_bonded: 3.49 restraints_weight: 0.1250 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30768 Z= 0.181 Angle : 0.592 7.117 41352 Z= 0.324 Chirality : 0.038 0.148 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.993 22.742 3984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.12 % Allowed : 6.84 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.24 (0.14), residues: 3576 helix: 4.07 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAx 63 TYR 0.022 0.003 TYRAc 39 PHE 0.018 0.002 PHEAg 41 TRP 0.009 0.001 TRPAn 93 HIS 0.005 0.001 HISAi 128 Details of bonding type rmsd covalent geometry : bond 0.00326 (30768) covalent geometry : angle 0.59229 (41352) hydrogen bonds : bond 0.08461 ( 2415) hydrogen bonds : angle 3.80134 ( 7245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 0.874 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7531 (mm-30) REVERT: Av 94 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7514 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7598 (mm-30) outliers start: 4 outliers final: 0 residues processed: 541 average time/residue: 1.0750 time to fit residues: 643.1056 Evaluate side-chains 537 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 335 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.137015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129300 restraints weight = 19386.793| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 0.56 r_work: 0.3371 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work: 0.3121 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30768 Z= 0.147 Angle : 0.533 6.554 41352 Z= 0.288 Chirality : 0.036 0.151 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.922 22.154 3984 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.64 (0.14), residues: 3576 helix: 4.36 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAx 63 TYR 0.017 0.002 TYRAp 39 PHE 0.010 0.001 PHEAl 41 TRP 0.009 0.001 TRPAw 93 HIS 0.003 0.001 HISAo 128 Details of bonding type rmsd covalent geometry : bond 0.00254 (30768) covalent geometry : angle 0.53310 (41352) hydrogen bonds : bond 0.06953 ( 2415) hydrogen bonds : angle 3.56375 ( 7245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.249 Fit side-chains REVERT: Al 94 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7362 (mm-30) REVERT: Av 94 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7335 (mm-30) REVERT: Aw 94 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7411 (mm-30) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 1.2076 time to fit residues: 719.8985 Evaluate side-chains 539 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 20 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 290 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.134914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127615 restraints weight = 19387.605| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.50 r_work: 0.3352 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.3101 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30768 Z= 0.161 Angle : 0.560 6.536 41352 Z= 0.303 Chirality : 0.037 0.148 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.940 22.364 3984 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.47 (0.14), residues: 3576 helix: 4.23 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.21 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAx 63 TYR 0.019 0.002 TYRAn 39 PHE 0.014 0.001 PHEAd 41 TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 Details of bonding type rmsd covalent geometry : bond 0.00282 (30768) covalent geometry : angle 0.55951 (41352) hydrogen bonds : bond 0.07648 ( 2415) hydrogen bonds : angle 3.67909 ( 7245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18646.29 seconds wall clock time: 316 minutes 40.07 seconds (19000.07 seconds total)