Starting phenix.real_space_refine on Tue May 27 08:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kay_62216/05_2025/9kay_62216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kay_62216/05_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_62216/05_2025/9kay_62216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kay_62216/05_2025/9kay_62216.map" model { file = "/net/cci-nas-00/data/ceres_data/9kay_62216/05_2025/9kay_62216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kay_62216/05_2025/9kay_62216.cif" } resolution = 1.73 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= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.56, per 1000 atoms: 0.58 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: 7.40 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.36 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: 8.96 Time building geometry restraints manager: 8.57 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: 3.450 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: 0.030 Extract box with map and model: 1.370 Check model and map are aligned: 0.220 Set scattering table: 0.370 Process input model: 61.450 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.180 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.410 ------------------------------------------------------------------------------- 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 (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: 5.22 (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 TRP 0.013 0.001 TRPAv 93 HIS 0.005 0.001 HISAk 105 PHE 0.018 0.002 PHEAx 41 TYR 0.025 0.003 TYRAc 39 ARG 0.002 0.000 ARGAk 76 Details of bonding type rmsd hydrogen bonds : bond 0.10087 ( 2415) hydrogen bonds : angle 4.00804 ( 7245) covalent geometry : bond 0.00320 (30768) covalent geometry : angle 0.62622 (41352) *********************** 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 : 3.658 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 547 average time/residue: 2.3202 time to fit residues: 1405.9059 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 : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ** Ag 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 14 GLN Ai 14 GLN Aj 14 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129802 restraints weight = 18930.099| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.31 r_work: 0.3380 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3138 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30768 Z= 0.154 Angle : 0.536 6.591 41352 Z= 0.295 Chirality : 0.036 0.152 4344 Planarity : 0.003 0.028 5400 Dihedral : 4.024 21.537 3984 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.88 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 (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: 5.50 (0.14), residues: 3576 helix: 4.27 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.14 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAn 93 HIS 0.003 0.001 HISAk 105 PHE 0.014 0.001 PHEAd 41 TYR 0.020 0.002 TYRAg 39 ARG 0.001 0.000 ARGAu 9 Details of bonding type rmsd hydrogen bonds : bond 0.07551 ( 2415) hydrogen bonds : angle 3.64865 ( 7245) covalent geometry : bond 0.00255 (30768) covalent geometry : angle 0.53607 (41352) *********************** 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 579 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 552 time to evaluate : 3.599 Fit side-chains REVERT: Aw 94 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7936 (mm-30) outliers start: 27 outliers final: 0 residues processed: 557 average time/residue: 2.2251 time to fit residues: 1374.1555 Evaluate side-chains 536 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 0.7980 chunk 150 optimal weight: 30.0000 chunk 205 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 344 optimal weight: 4.9990 chunk 279 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aj 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124708 restraints weight = 18973.906| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 0.31 r_work: 0.3316 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3071 rms_B_bonded: 3.00 restraints_weight: 0.1250 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 30768 Z= 0.223 Angle : 0.648 8.083 41352 Z= 0.360 Chirality : 0.041 0.151 4344 Planarity : 0.004 0.029 5400 Dihedral : 4.115 21.106 3984 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.16 % Allowed : 4.99 % Favored : 93.86 % 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: 4.74 (0.14), residues: 3576 helix: 3.71 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.07 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAl 93 HIS 0.006 0.002 HISAi 128 PHE 0.024 0.002 PHEAx 41 TYR 0.027 0.004 TYRAc 39 ARG 0.003 0.001 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.09520 ( 2415) hydrogen bonds : angle 3.97591 ( 7245) covalent geometry : bond 0.00423 (30768) covalent geometry : angle 0.64790 (41352) *********************** 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 598 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 560 time to evaluate : 3.896 Fit side-chains REVERT: Aq 117 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8870 (tt) outliers start: 38 outliers final: 0 residues processed: 566 average time/residue: 2.2149 time to fit residues: 1392.1300 Evaluate side-chains 558 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aq residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 313 optimal weight: 0.6980 chunk 148 optimal weight: 0.1980 chunk 296 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 318 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.133481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128096 restraints weight = 19034.988| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.32 r_work: 0.3358 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3114 rms_B_bonded: 3.04 restraints_weight: 0.1250 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 30768 Z= 0.163 Angle : 0.545 6.751 41352 Z= 0.301 Chirality : 0.037 0.153 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.020 21.578 3984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.85 % Allowed : 5.87 % Favored : 93.28 % 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: 5.22 (0.14), residues: 3576 helix: 4.06 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.11 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAi 128 PHE 0.015 0.002 PHEAd 41 TYR 0.020 0.003 TYRAf 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08002 ( 2415) hydrogen bonds : angle 3.75381 ( 7245) covalent geometry : bond 0.00271 (30768) covalent geometry : angle 0.54456 (41352) *********************** 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 562 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 534 time to evaluate : 3.740 Fit side-chains outliers start: 28 outliers final: 0 residues processed: 538 average time/residue: 2.2597 time to fit residues: 1347.9055 Evaluate side-chains 535 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 45 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 333 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125269 restraints weight = 18985.486| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 0.31 r_work: 0.3323 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3079 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30768 Z= 0.206 Angle : 0.621 7.749 41352 Z= 0.344 Chirality : 0.039 0.153 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.075 20.923 3984 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.67 % 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: 4.82 (0.14), residues: 3576 helix: 3.78 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.04 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAn 93 HIS 0.006 0.002 HISAi 128 PHE 0.021 0.002 PHEAx 41 TYR 0.024 0.003 TYRAc 39 ARG 0.003 0.001 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.09213 ( 2415) hydrogen bonds : angle 3.93634 ( 7245) covalent geometry : bond 0.00382 (30768) covalent geometry : angle 0.62086 (41352) *********************** 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 563 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 558 time to evaluate : 3.647 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 562 average time/residue: 2.2317 time to fit residues: 1391.5841 Evaluate side-chains 560 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 18 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.132588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127208 restraints weight = 18945.766| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.31 r_work: 0.3347 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3103 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0495 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= 0.174 Angle : 0.570 7.007 41352 Z= 0.314 Chirality : 0.037 0.154 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.029 21.485 3984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.12 % Allowed : 6.48 % 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 (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: 5.14 (0.14), residues: 3576 helix: 4.01 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.10 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 PHE 0.017 0.002 PHEAl 41 TYR 0.021 0.003 TYRAa 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08311 ( 2415) hydrogen bonds : angle 3.79619 ( 7245) covalent geometry : bond 0.00302 (30768) covalent geometry : angle 0.57019 (41352) *********************** 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 541 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 3.679 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 541 average time/residue: 2.2974 time to fit residues: 1376.1078 Evaluate side-chains 535 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.133488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128185 restraints weight = 18958.439| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.31 r_work: 0.3360 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3116 rms_B_bonded: 3.03 restraints_weight: 0.1250 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30768 Z= 0.166 Angle : 0.560 6.804 41352 Z= 0.307 Chirality : 0.037 0.153 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.999 21.791 3984 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.24 % Allowed : 6.69 % Favored : 93.07 % 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: 5.28 (0.14), residues: 3576 helix: 4.11 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.11 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 PHE 0.015 0.002 PHEAg 41 TYR 0.020 0.002 TYRAa 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.07988 ( 2415) hydrogen bonds : angle 3.74705 ( 7245) covalent geometry : bond 0.00289 (30768) covalent geometry : angle 0.55964 (41352) *********************** 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 544 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 536 time to evaluate : 3.569 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 540 average time/residue: 2.2753 time to fit residues: 1360.1823 Evaluate side-chains 535 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 203 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 305 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 287 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 229 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.132389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127079 restraints weight = 18959.124| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.31 r_work: 0.3346 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3102 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30768 Z= 0.179 Angle : 0.588 7.075 41352 Z= 0.321 Chirality : 0.038 0.151 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.023 21.804 3984 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.88 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 (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: 5.13 (0.14), residues: 3576 helix: 4.00 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.09 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.005 0.001 HISAo 128 PHE 0.017 0.002 PHEAg 41 TYR 0.021 0.003 TYRAc 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08422 ( 2415) hydrogen bonds : angle 3.80967 ( 7245) covalent geometry : bond 0.00318 (30768) covalent geometry : angle 0.58769 (41352) *********************** 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 539 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 535 time to evaluate : 3.697 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 539 average time/residue: 2.3409 time to fit residues: 1399.2113 Evaluate side-chains 535 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 342 optimal weight: 0.6980 chunk 229 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.135367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130043 restraints weight = 18967.020| |-----------------------------------------------------------------------------| r_work (start): 0.3453 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: 0.3140 rms_B_bonded: 3.03 restraints_weight: 0.1250 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0628 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= 0.154 Angle : 0.544 6.397 41352 Z= 0.295 Chirality : 0.036 0.150 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.970 21.881 3984 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 (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: 5.46 (0.14), residues: 3576 helix: 4.24 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAn 93 HIS 0.003 0.001 HISAo 128 PHE 0.012 0.001 PHEAl 41 TYR 0.018 0.002 TYRAw 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.07368 ( 2415) hydrogen bonds : angle 3.65083 ( 7245) covalent geometry : bond 0.00267 (30768) covalent geometry : angle 0.54433 (41352) *********************** 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 540 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 536 time to evaluate : 3.992 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 540 average time/residue: 2.2425 time to fit residues: 1341.2906 Evaluate side-chains 535 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 48 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 203 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 319 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.136186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128891 restraints weight = 19749.865| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.52 r_work: 0.3388 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3148 rms_B_bonded: 3.60 restraints_weight: 0.1250 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30768 Z= 0.166 Angle : 0.570 6.726 41352 Z= 0.309 Chirality : 0.037 0.150 4344 Planarity : 0.003 0.027 5400 Dihedral : 3.985 22.391 3984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.18 % Allowed : 6.84 % Favored : 92.97 % 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: 5.32 (0.14), residues: 3576 helix: 4.14 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 PHE 0.014 0.001 PHEAg 41 TYR 0.019 0.002 TYRAe 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.07890 ( 2415) hydrogen bonds : angle 3.73029 ( 7245) covalent geometry : bond 0.00291 (30768) covalent geometry : angle 0.57008 (41352) ********************** 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 542 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 536 time to evaluate : 3.667 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 536 average time/residue: 2.2522 time to fit residues: 1339.0793 Evaluate side-chains 542 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 536 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Af residue 147 LYS Chi-restraints excluded: chain Ai residue 147 LYS Chi-restraints excluded: chain As residue 147 LYS Chi-restraints excluded: chain Au residue 147 LYS Chi-restraints excluded: chain Aw residue 147 LYS Chi-restraints excluded: chain Ax residue 147 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 38 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.137442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130441 restraints weight = 19722.295| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 0.49 r_work: 0.3408 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3166 rms_B_bonded: 3.52 restraints_weight: 0.1250 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0649 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= 0.156 Angle : 0.551 6.382 41352 Z= 0.298 Chirality : 0.036 0.150 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.965 22.473 3984 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.46 % Allowed : 6.57 % Favored : 92.97 % 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: 5.43 (0.14), residues: 3576 helix: 4.21 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.18 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAl 93 HIS 0.003 0.001 HISAo 128 PHE 0.012 0.001 PHEAl 41 TYR 0.018 0.002 TYRAw 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.07433 ( 2415) hydrogen bonds : angle 3.65537 ( 7245) covalent geometry : bond 0.00273 (30768) covalent geometry : angle 0.55148 (41352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38314.84 seconds wall clock time: 656 minutes 55.03 seconds (39415.03 seconds total)