Starting phenix.real_space_refine on Wed Jun 25 07:44:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kay_62216/06_2025/9kay_62216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kay_62216/06_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_62216/06_2025/9kay_62216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kay_62216/06_2025/9kay_62216.map" model { file = "/net/cci-nas-00/data/ceres_data/9kay_62216/06_2025/9kay_62216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kay_62216/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.12, per 1000 atoms: 0.57 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: 6.77 Conformation dependent library (CDL) restraints added in 3.5 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: 2.28 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: 9.17 Time building geometry restraints manager: 8.09 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 60.290 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.760 ------------------------------------------------------------------------------- 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 : 3.258 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 547 average time/residue: 2.6244 time to fit residues: 1592.4590 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 : 4.885 ------------------------------------------------------------------------------- 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 = 0.135083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129811 restraints weight = 18930.673| |-----------------------------------------------------------------------------| 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: 0.3139 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work (final): 0.3139 ------------------------------------------------------------------------------- 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 : 3.502 Fit side-chains REVERT: Aw 94 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7941 (mm-30) outliers start: 27 outliers final: 0 residues processed: 557 average time/residue: 2.2860 time to fit residues: 1411.1418 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 : 3.256 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 344 optimal weight: 4.9990 chunk 279 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126228 restraints weight = 18948.378| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 0.31 r_work: 0.3336 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3091 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30768 Z= 0.190 Angle : 0.597 7.532 41352 Z= 0.331 Chirality : 0.039 0.153 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.058 21.147 3984 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.64 % Allowed : 5.60 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.05 (0.14), residues: 3576 helix: 3.94 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.12 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAl 93 HIS 0.005 0.001 HISAi 128 PHE 0.019 0.002 PHEAg 41 TYR 0.024 0.003 TYRAc 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08843 ( 2415) hydrogen bonds : angle 3.85994 ( 7245) covalent geometry : bond 0.00339 (30768) covalent geometry : angle 0.59651 (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 581 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 560 time to evaluate : 3.479 Fit side-chains outliers start: 21 outliers final: 0 residues processed: 566 average time/residue: 2.3015 time to fit residues: 1444.6308 Evaluate side-chains 542 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 296 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 324 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 chunk 223 optimal weight: 0.3980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130436 restraints weight = 19107.269| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.32 r_work: 0.3388 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.3144 rms_B_bonded: 3.06 restraints_weight: 0.1250 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0601 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= 0.147 Angle : 0.515 6.381 41352 Z= 0.283 Chirality : 0.036 0.147 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.961 21.653 3984 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.85 % Allowed : 5.84 % Favored : 93.31 % 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: 5.54 (0.14), residues: 3576 helix: 4.29 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.17 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAn 93 HIS 0.003 0.001 HISAi 128 PHE 0.012 0.001 PHEAl 41 TYR 0.018 0.002 TYRAw 39 ARG 0.001 0.000 ARGAt 43 Details of bonding type rmsd hydrogen bonds : bond 0.07281 ( 2415) hydrogen bonds : angle 3.61281 ( 7245) covalent geometry : bond 0.00241 (30768) covalent geometry : angle 0.51479 (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 566 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 538 time to evaluate : 3.408 Fit side-chains outliers start: 28 outliers final: 0 residues processed: 542 average time/residue: 2.5472 time to fit residues: 1527.9193 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 : 3.990 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 332 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.133731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126440 restraints weight = 19612.359| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.52 r_work: 0.3358 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3117 rms_B_bonded: 3.55 restraints_weight: 0.1250 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0544 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= 0.192 Angle : 0.599 7.442 41352 Z= 0.331 Chirality : 0.038 0.151 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.031 22.053 3984 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.85 % Allowed : 5.75 % 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: 5.08 (0.14), residues: 3576 helix: 3.96 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.12 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAl 93 HIS 0.005 0.001 HISAi 128 PHE 0.020 0.002 PHEAx 41 TYR 0.023 0.003 TYRAc 39 ARG 0.003 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08829 ( 2415) hydrogen bonds : angle 3.85903 ( 7245) covalent geometry : bond 0.00347 (30768) covalent geometry : angle 0.59892 (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 588 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 560 time to evaluate : 3.464 Fit side-chains outliers start: 28 outliers final: 0 residues processed: 564 average time/residue: 2.3132 time to fit residues: 1447.0420 Evaluate side-chains 552 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 3.489 ------------------------------------------------------------------------------- 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: 2.9990 chunk 190 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 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 = 0.3550 r_free = 0.3550 target = 0.135032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127729 restraints weight = 19649.418| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.52 r_work: 0.3374 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3132 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0539 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= 0.173 Angle : 0.569 7.020 41352 Z= 0.313 Chirality : 0.037 0.152 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.014 22.404 3984 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.76 % Allowed : 5.35 % Favored : 93.89 % 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: 5.21 (0.14), residues: 3576 helix: 4.05 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.12 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAl 93 HIS 0.004 0.001 HISAi 128 PHE 0.016 0.002 PHEAl 41 TYR 0.021 0.003 TYRAc 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08287 ( 2415) hydrogen bonds : angle 3.78336 ( 7245) covalent geometry : bond 0.00302 (30768) covalent geometry : angle 0.56869 (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 564 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 539 time to evaluate : 3.411 Fit side-chains outliers start: 25 outliers final: 0 residues processed: 543 average time/residue: 2.3220 time to fit residues: 1394.4568 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 : 3.525 ------------------------------------------------------------------------------- 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: 4.9990 chunk 160 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 255 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.133895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126611 restraints weight = 19623.113| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.52 r_work: 0.3363 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3121 rms_B_bonded: 3.57 restraints_weight: 0.1250 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0554 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= 0.190 Angle : 0.600 7.357 41352 Z= 0.330 Chirality : 0.038 0.152 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.045 22.346 3984 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % 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: 5.04 (0.14), residues: 3576 helix: 3.93 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.08 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAl 93 HIS 0.005 0.001 HISAi 128 PHE 0.018 0.002 PHEAg 41 TYR 0.023 0.003 TYRAc 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08778 ( 2415) hydrogen bonds : angle 3.86078 ( 7245) covalent geometry : bond 0.00344 (30768) covalent geometry : angle 0.60004 (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 564 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 560 time to evaluate : 3.861 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 564 average time/residue: 2.4353 time to fit residues: 1524.9930 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 : 3.632 ------------------------------------------------------------------------------- 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: 8.9990 chunk 295 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 355 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125864 restraints weight = 19609.911| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.52 r_work: 0.3354 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3112 rms_B_bonded: 3.56 restraints_weight: 0.1250 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30768 Z= 0.204 Angle : 0.625 7.660 41352 Z= 0.344 Chirality : 0.039 0.152 4344 Planarity : 0.004 0.028 5400 Dihedral : 4.074 22.204 3984 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.94 % Allowed : 6.02 % 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: 4.88 (0.14), residues: 3576 helix: 3.82 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.05 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAl 93 HIS 0.005 0.002 HISAi 128 PHE 0.020 0.002 PHEAx 41 TYR 0.024 0.003 TYRAe 39 ARG 0.003 0.001 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.09122 ( 2415) hydrogen bonds : angle 3.91458 ( 7245) covalent geometry : bond 0.00380 (30768) covalent geometry : angle 0.62458 (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 591 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 560 time to evaluate : 3.416 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 564 average time/residue: 2.7734 time to fit residues: 1748.0870 Evaluate side-chains 565 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 547 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 147 LYS Chi-restraints excluded: chain Ac residue 147 LYS Chi-restraints excluded: chain Ad residue 147 LYS Chi-restraints excluded: chain Ae residue 147 LYS Chi-restraints excluded: chain Ag residue 147 LYS Chi-restraints excluded: chain Ah residue 147 LYS Chi-restraints excluded: chain Ai residue 147 LYS Chi-restraints excluded: chain Aj residue 147 LYS Chi-restraints excluded: chain Ak residue 147 LYS Chi-restraints excluded: chain Al residue 147 LYS Chi-restraints excluded: chain An residue 147 LYS Chi-restraints excluded: chain Ao residue 147 LYS Chi-restraints excluded: chain Aq residue 147 LYS Chi-restraints excluded: chain Ar residue 147 LYS Chi-restraints excluded: chain Au residue 147 LYS Chi-restraints excluded: chain Av residue 147 LYS Chi-restraints excluded: chain Aw residue 147 LYS Chi-restraints excluded: chain Ax residue 147 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.135287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127998 restraints weight = 19637.968| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 0.52 r_work: 0.3381 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3139 rms_B_bonded: 3.60 restraints_weight: 0.1250 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30768 Z= 0.173 Angle : 0.577 6.912 41352 Z= 0.315 Chirality : 0.037 0.155 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.025 22.430 3984 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.82 % Allowed : 6.17 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.21 (0.14), residues: 3576 helix: 4.06 (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 0.010 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 PHE 0.016 0.002 PHEAl 41 TYR 0.020 0.003 TYRAs 39 ARG 0.002 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08178 ( 2415) hydrogen bonds : angle 3.78071 ( 7245) covalent geometry : bond 0.00305 (30768) covalent geometry : angle 0.57725 (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 563 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 536 time to evaluate : 3.608 Fit side-chains outliers start: 27 outliers final: 0 residues processed: 540 average time/residue: 2.3118 time to fit residues: 1382.7880 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 : 3.334 ------------------------------------------------------------------------------- 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: 4.9990 chunk 301 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.135678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128390 restraints weight = 19698.736| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 0.52 r_work: 0.3382 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3142 rms_B_bonded: 3.59 restraints_weight: 0.1250 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30768 Z= 0.170 Angle : 0.576 6.812 41352 Z= 0.313 Chirality : 0.037 0.152 4344 Planarity : 0.003 0.027 5400 Dihedral : 4.008 22.601 3984 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.12 % Allowed : 6.87 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.28 (0.14), residues: 3576 helix: 4.11 (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 0.010 0.001 TRPAl 93 HIS 0.004 0.001 HISAo 128 PHE 0.015 0.002 PHEAg 41 TYR 0.020 0.003 TYRAs 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.08042 ( 2415) hydrogen bonds : angle 3.76082 ( 7245) covalent geometry : bond 0.00299 (30768) covalent geometry : angle 0.57582 (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 540 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 536 time to evaluate : 3.413 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 540 average time/residue: 2.3616 time to fit residues: 1414.7833 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 : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 38 optimal weight: 0.5980 chunk 187 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133118 restraints weight = 19907.384| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 0.52 r_work: 0.3451 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3212 rms_B_bonded: 3.67 restraints_weight: 0.1250 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30768 Z= 0.140 Angle : 0.526 6.802 41352 Z= 0.282 Chirality : 0.035 0.150 4344 Planarity : 0.003 0.026 5400 Dihedral : 3.917 22.025 3984 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.03 % Allowed : 6.93 % 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: 5.68 (0.14), residues: 3576 helix: 4.40 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : 0.19 (0.30), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAw 93 HIS 0.003 0.001 HISAo 128 PHE 0.009 0.001 PHEAv 41 TYR 0.015 0.002 TYRAt 39 ARG 0.001 0.000 ARGAx 63 Details of bonding type rmsd hydrogen bonds : bond 0.06517 ( 2415) hydrogen bonds : angle 3.50068 ( 7245) covalent geometry : bond 0.00243 (30768) covalent geometry : angle 0.52597 (41352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42054.17 seconds wall clock time: 730 minutes 51.32 seconds (43851.32 seconds total)