Starting phenix.real_space_refine (version: dev) on Mon Dec 12 04:18:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2022/3j89_6123.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.047 sd= 0.273 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9025 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 4.26, per 1000 atoms: 0.47 Number of scatterers: 9025 At special positions: 0 Unit cell: (90.78, 90.78, 67.32, 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) O 817 8.00 N 855 7.00 C 2755 6.00 H 4598 1.00 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 - 3.50 Amino acid : False - 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: 7.00 Conformation dependent library (CDL) restraints added in 703.5 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 96.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.543A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA P 7 " --> pdb=" O ARG P 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA Q 7 " --> pdb=" O ARG Q 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA R 7 " --> pdb=" O ARG R 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.08: 1102 1.08 - 1.19: 3496 1.19 - 1.31: 928 1.31 - 1.43: 1005 1.43 - 1.54: 2513 Bond restraints: 9044 Sorted by residual: bond pdb=" N ALA P 7 " pdb=" H ALA P 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" N ALA D 7 " pdb=" H ALA D 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" N ALA J 7 " pdb=" H ALA J 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA E 7 " pdb=" H ALA E 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA F 7 " pdb=" H ALA F 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 104.85 - 110.43: 9584 110.43 - 116.01: 1683 116.01 - 121.59: 3836 121.59 - 127.17: 1161 127.17 - 132.76: 76 Bond angle restraints: 16340 Sorted by residual: angle pdb=" N ILE R 4 " pdb=" CA ILE R 4 " pdb=" C ILE R 4 " ideal model delta sigma weight residual 112.83 108.63 4.20 9.90e-01 1.02e+00 1.80e+01 angle pdb=" N ILE C 4 " pdb=" CA ILE C 4 " pdb=" C ILE C 4 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.76e+01 angle pdb=" N ILE Q 4 " pdb=" CA ILE Q 4 " pdb=" C ILE Q 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE K 4 " pdb=" CA ILE K 4 " pdb=" C ILE K 4 " ideal model delta sigma weight residual 112.83 108.71 4.12 9.90e-01 1.02e+00 1.73e+01 ... (remaining 16335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 3313 11.65 - 23.30: 221 23.30 - 34.95: 38 34.95 - 46.59: 19 46.59 - 58.24: 19 Dihedral angle restraints: 3610 sinusoidal: 1824 harmonic: 1786 Sorted by residual: dihedral pdb=" CA ILE C 4 " pdb=" C ILE C 4 " pdb=" N LEU C 5 " pdb=" CA LEU C 5 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE F 4 " pdb=" C ILE F 4 " pdb=" N LEU F 5 " pdb=" CA LEU F 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE O 4 " pdb=" C ILE O 4 " pdb=" N LEU O 5 " pdb=" CA LEU O 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 119 0.040 - 0.079: 197 0.079 - 0.118: 208 0.118 - 0.157: 109 0.157 - 0.197: 70 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA GLU N 10 " pdb=" N GLU N 10 " pdb=" C GLU N 10 " pdb=" CB GLU N 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA GLU O 10 " pdb=" N GLU O 10 " pdb=" C GLU O 10 " pdb=" CB GLU O 10 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 700 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 22 " 0.020 2.00e-02 2.50e+03 3.11e-02 2.18e+01 pdb=" CG HIS E 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS E 22 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS E 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 22 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS E 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS E 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS E 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 22 " 0.020 2.00e-02 2.50e+03 3.10e-02 2.17e+01 pdb=" CG HIS H 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS H 22 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS H 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS H 22 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS H 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS H 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS H 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS H 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 22 " -0.019 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" CG HIS R 22 " -0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS R 22 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS R 22 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS R 22 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS R 22 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS R 22 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 HIS R 22 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS R 22 " -0.018 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.29: 1304 2.29 - 2.84: 20083 2.84 - 3.40: 22086 3.40 - 3.95: 29734 3.95 - 4.50: 42641 Nonbonded interactions: 115848 Sorted by model distance: nonbonded pdb="HH22 ARG H 3 " pdb=" OE1 GLU H 6 " model vdw 1.738 1.850 nonbonded pdb="HH22 ARG S 3 " pdb=" OE1 GLU S 6 " model vdw 1.738 1.850 nonbonded pdb="HH22 ARG Q 3 " pdb=" OE1 GLU Q 6 " model vdw 1.738 1.850 nonbonded pdb="HH22 ARG N 3 " pdb=" OE1 GLU N 6 " model vdw 1.738 1.850 nonbonded pdb="HH22 ARG M 3 " pdb=" OE1 GLU M 6 " model vdw 1.738 1.850 ... (remaining 115843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 2755 2.51 5 N 855 2.21 5 O 817 1.98 5 H 4598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.120 Extract box with map and model: 1.030 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 30.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.022 0.065 4446 Z= 1.471 Angle : 1.639 5.689 5985 Z= 1.159 Chirality : 0.101 0.197 703 Planarity : 0.010 0.046 798 Dihedral : 11.967 58.243 1710 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.00 % 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: -0.96 (0.29), residues: 513 helix: -0.44 (0.18), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.5452 time to fit residues: 89.5279 Evaluate side-chains 75 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN O 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 4446 Z= 0.319 Angle : 0.637 5.550 5985 Z= 0.360 Chirality : 0.030 0.082 703 Planarity : 0.006 0.037 798 Dihedral : 4.860 16.981 646 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.51 % 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: 2.55 (0.34), residues: 513 helix: 1.72 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 134 average time/residue: 0.5407 time to fit residues: 83.9472 Evaluate side-chains 109 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1282 time to fit residues: 2.5033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4446 Z= 0.235 Angle : 0.513 4.352 5985 Z= 0.300 Chirality : 0.029 0.090 703 Planarity : 0.004 0.033 798 Dihedral : 4.428 15.406 646 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer Outliers : 2.76 % 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: 3.30 (0.34), residues: 513 helix: 2.18 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 0.5325 time to fit residues: 72.7074 Evaluate side-chains 105 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1123 time to fit residues: 1.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 4446 Z= 0.424 Angle : 0.687 6.623 5985 Z= 0.400 Chirality : 0.034 0.104 703 Planarity : 0.007 0.049 798 Dihedral : 4.961 17.562 646 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 4.26 % 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: 1.49 (0.34), residues: 513 helix: 1.07 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.6213 time to fit residues: 63.9667 Evaluate side-chains 85 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1001 time to fit residues: 2.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4446 Z= 0.211 Angle : 0.480 4.055 5985 Z= 0.284 Chirality : 0.029 0.131 703 Planarity : 0.004 0.028 798 Dihedral : 4.405 16.881 646 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer Outliers : 1.75 % 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: 2.84 (0.34), residues: 513 helix: 1.90 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 98 average time/residue: 0.5705 time to fit residues: 64.6234 Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1120 time to fit residues: 2.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 4446 Z= 0.334 Angle : 0.575 5.484 5985 Z= 0.341 Chirality : 0.031 0.096 703 Planarity : 0.005 0.032 798 Dihedral : 4.689 20.791 646 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.51 % 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: 2.01 (0.34), residues: 513 helix: 1.39 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 89 average time/residue: 0.5977 time to fit residues: 61.2693 Evaluate side-chains 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1148 time to fit residues: 2.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.036 4446 Z= 0.397 Angle : 0.619 6.109 5985 Z= 0.368 Chirality : 0.033 0.124 703 Planarity : 0.006 0.036 798 Dihedral : 4.920 24.571 646 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.76 % 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: 1.41 (0.34), residues: 513 helix: 1.01 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.6361 time to fit residues: 60.4825 Evaluate side-chains 82 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.729 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2185 time to fit residues: 2.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4446 Z= 0.271 Angle : 0.520 4.852 5985 Z= 0.310 Chirality : 0.030 0.156 703 Planarity : 0.005 0.029 798 Dihedral : 4.606 23.114 646 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.75 % 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: 2.18 (0.34), residues: 513 helix: 1.49 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.6229 time to fit residues: 66.9907 Evaluate side-chains 89 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1140 time to fit residues: 1.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4446 Z= 0.199 Angle : 0.466 4.038 5985 Z= 0.278 Chirality : 0.029 0.090 703 Planarity : 0.004 0.053 798 Dihedral : 4.364 22.235 646 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer Outliers : 1.75 % 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: 2.83 (0.34), residues: 513 helix: 1.89 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.5970 time to fit residues: 67.3284 Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1130 time to fit residues: 2.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 4446 Z= 0.192 Angle : 0.464 3.912 5985 Z= 0.276 Chirality : 0.029 0.101 703 Planarity : 0.004 0.043 798 Dihedral : 4.340 28.213 646 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.34), residues: 513 helix: 2.05 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.5884 time to fit residues: 67.1285 Evaluate side-chains 92 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1031 time to fit residues: 0.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089390 restraints weight = 28155.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092650 restraints weight = 14407.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094612 restraints weight = 10018.443| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4446 Z= 0.292 Angle : 0.542 4.939 5985 Z= 0.322 Chirality : 0.030 0.096 703 Planarity : 0.005 0.040 798 Dihedral : 4.616 26.000 646 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.34), residues: 513 helix: 1.68 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 2142.38 seconds wall clock time: 38 minutes 22.73 seconds (2302.73 seconds total)