Starting phenix.real_space_refine on Fri Dec 8 19:07:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2023/3j89_6123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2023/3j89_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_2023/3j89_6123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2023/3j89_6123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2023/3j89_6123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/12_2023/3j89_6123.pdb" } resolution = 3.6 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= 0.047 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 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. 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.52, per 1000 atoms: 0.50 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: 7.14 Conformation dependent library (CDL) restraints added in 839.7 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: 0.60 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: 3.13 Time building geometry restraints manager: 7.44 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: 3693 11.65 - 23.30: 221 23.30 - 34.95: 38 34.95 - 46.59: 19 46.59 - 58.24: 19 Dihedral angle restraints: 3990 sinusoidal: 2204 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 3987 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 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: 0.060 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: 0.130 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.220 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.29), residues: 513 helix: -0.44 (0.18), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 22 TYR 0.015 0.006 TYR F 15 ARG 0.003 0.001 ARG A 17 *********************** 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 : 0.667 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: 0.6584 time to fit residues: 106.6618 Evaluate side-chains 75 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8887 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 5.9990 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: 7.9990 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 R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4130 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= 0.377 Angle : 0.674 5.751 5985 Z= 0.375 Chirality : 0.029 0.076 703 Planarity : 0.006 0.033 798 Dihedral : 4.869 17.155 646 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.76 % Allowed : 13.28 % Favored : 83.96 % 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: 2.58 (0.34), residues: 513 helix: 1.74 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 22 TYR 0.013 0.003 TYR R 15 ARG 0.008 0.001 ARG M 13 *********************** 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 138 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.768 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: 11 outliers final: 9 residues processed: 132 average time/residue: 0.6629 time to fit residues: 99.2398 Evaluate side-chains 106 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1140 time to fit residues: 2.6244 ------------------------------------------------------------------------------- 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: 7.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.5155 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= 0.238 Angle : 0.520 4.492 5985 Z= 0.304 Chirality : 0.029 0.091 703 Planarity : 0.004 0.025 798 Dihedral : 4.437 15.469 646 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.01 % Allowed : 21.55 % Favored : 76.44 % 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: 3.19 (0.34), residues: 513 helix: 2.11 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.003 TYR R 15 ARG 0.005 0.001 ARG A 13 *********************** 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: 8 poor density : 115 time to evaluate : 0.808 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 outliers start: 8 outliers final: 4 residues processed: 119 average time/residue: 0.6231 time to fit residues: 84.9667 Evaluate side-chains 105 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1015 time to fit residues: 1.4828 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- 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: 0.8196 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4446 Z= 0.286 Angle : 0.558 4.951 5985 Z= 0.326 Chirality : 0.029 0.113 703 Planarity : 0.005 0.035 798 Dihedral : 4.549 16.756 646 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.26 % Allowed : 21.55 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.34), residues: 513 helix: 1.81 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 22 TYR 0.018 0.004 TYR F 15 ARG 0.006 0.001 ARG M 27 *********************** 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 115 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.7390 time to fit residues: 88.5959 Evaluate side-chains 103 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1096 time to fit residues: 3.7314 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4446 Z= 0.255 Angle : 0.511 4.457 5985 Z= 0.304 Chirality : 0.029 0.102 703 Planarity : 0.004 0.030 798 Dihedral : 4.419 15.864 646 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.75 % Allowed : 24.06 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.34), residues: 513 helix: 1.90 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.016 0.004 TYR E 15 ARG 0.005 0.001 ARG M 27 *********************** 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 102 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.6723 time to fit residues: 74.4038 Evaluate side-chains 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1215 time to fit residues: 2.1177 ------------------------------------------------------------------------------- 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: 10.0000 chunk 36 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.8213 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4446 Z= 0.371 Angle : 0.614 6.175 5985 Z= 0.361 Chirality : 0.032 0.090 703 Planarity : 0.006 0.040 798 Dihedral : 4.753 18.663 646 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.76 % Allowed : 24.06 % Favored : 73.18 % 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: 1.92 (0.34), residues: 513 helix: 1.33 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS P 22 TYR 0.022 0.005 TYR C 15 ARG 0.006 0.001 ARG A 13 *********************** 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 90 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.7786 time to fit residues: 74.0545 Evaluate side-chains 82 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1061 time to fit residues: 2.4891 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.8199 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4446 Z= 0.303 Angle : 0.545 5.142 5985 Z= 0.324 Chirality : 0.030 0.125 703 Planarity : 0.005 0.029 798 Dihedral : 4.612 21.061 646 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.76 % Allowed : 24.81 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.34), residues: 513 helix: 1.49 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS P 22 TYR 0.016 0.004 TYR E 15 ARG 0.005 0.001 ARG M 27 *********************** 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 95 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.7437 time to fit residues: 77.4433 Evaluate side-chains 88 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1170 time to fit residues: 2.2279 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4446 Z= 0.173 Angle : 0.438 3.349 5985 Z= 0.261 Chirality : 0.028 0.094 703 Planarity : 0.004 0.025 798 Dihedral : 4.113 19.297 646 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.01 % Allowed : 25.56 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.23 (0.34), residues: 513 helix: 2.14 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 22 TYR 0.012 0.003 TYR C 15 ARG 0.006 0.000 ARG E 27 *********************** 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 111 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 104 average time/residue: 0.6776 time to fit residues: 80.2721 Evaluate side-chains 100 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1174 time to fit residues: 2.2799 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4446 Z= 0.293 Angle : 0.546 5.025 5985 Z= 0.325 Chirality : 0.030 0.097 703 Planarity : 0.005 0.029 798 Dihedral : 4.619 30.564 646 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.25 % Allowed : 26.32 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS P 22 TYR 0.016 0.004 TYR N 15 ARG 0.005 0.001 ARG E 27 *********************** 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 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.6994 time to fit residues: 70.7560 Evaluate side-chains 86 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1182 time to fit residues: 1.8553 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4446 Z= 0.203 Angle : 0.472 3.928 5985 Z= 0.280 Chirality : 0.029 0.113 703 Planarity : 0.004 0.024 798 Dihedral : 4.250 24.157 646 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.50 % Allowed : 26.57 % Favored : 71.93 % 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: 3.10 (0.34), residues: 513 helix: 2.06 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.003 TYR C 15 ARG 0.005 0.000 ARG M 27 ********************** 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: 6 poor density : 93 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 0.7313 time to fit residues: 78.2267 Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1208 time to fit residues: 1.8317 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.115120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093030 restraints weight = 27768.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096482 restraints weight = 13792.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098573 restraints weight = 9379.566| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4446 Z= 0.259 Angle : 0.517 4.672 5985 Z= 0.308 Chirality : 0.030 0.119 703 Planarity : 0.005 0.026 798 Dihedral : 4.434 25.707 646 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.25 % Allowed : 26.82 % Favored : 71.93 % 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: 2.80 (0.34), residues: 513 helix: 1.87 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.014 0.004 TYR K 15 ARG 0.004 0.001 ARG M 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.20 seconds wall clock time: 42 minutes 27.36 seconds (2547.36 seconds total)