Starting phenix.real_space_refine on Tue Aug 4 21:41:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr1_36590/08_2026/8jr1_36590.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Br 7 7.06 5 S 33 5.16 5 C 4712 2.51 5 N 1118 2.21 5 O 1212 1.98 5 F 7 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7089 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "2" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "3" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "4" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "5" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "6" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "7" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "8" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "9" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.23 Number of scatterers: 7089 At special positions: 0 Unit cell: (73, 98.55, 82.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 7 34.99 S 33 16.00 F 7 9.00 O 1212 8.00 N 1118 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 364.8 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 1 sheets defined 87.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain '1' and resid 1 through 42 removed outlier: 4.180A pdb=" N ILE 1 5 " --> pdb=" O MET 1 1 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 76 removed outlier: 4.161A pdb=" N PHE 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR 1 51 " --> pdb=" O GLY 1 47 " (cutoff:3.500A) Proline residue: 1 52 - end of helix removed outlier: 3.537A pdb=" N TYR 1 64 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN 1 67 " --> pdb=" O ALA 1 63 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 42 removed outlier: 3.568A pdb=" N GLY 2 29 " --> pdb=" O GLY 2 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 77 removed outlier: 3.529A pdb=" N PHE 2 50 " --> pdb=" O GLN 2 46 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix removed outlier: 3.619A pdb=" N ALA 2 62 " --> pdb=" O GLY 2 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 42 removed outlier: 3.846A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER 3 37 " --> pdb=" O ASN 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 76 removed outlier: 4.776A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix removed outlier: 3.532A pdb=" N ILE 3 55 " --> pdb=" O THR 3 51 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 3 62 " --> pdb=" O GLY 3 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN 3 67 " --> pdb=" O ALA 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 42 removed outlier: 3.530A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 77 removed outlier: 4.762A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix removed outlier: 3.789A pdb=" N ILE 4 55 " --> pdb=" O THR 4 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR 4 56 " --> pdb=" O PRO 4 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 4 63 " --> pdb=" O LEU 4 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN 4 67 " --> pdb=" O ALA 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 42 removed outlier: 3.557A pdb=" N ILE 5 26 " --> pdb=" O ILE 5 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 78 removed outlier: 3.927A pdb=" N PHE 5 50 " --> pdb=" O GLN 5 46 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix removed outlier: 3.824A pdb=" N ILE 5 55 " --> pdb=" O THR 5 51 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN 5 67 " --> pdb=" O ALA 5 63 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 42 removed outlier: 4.022A pdb=" N ALA 6 6 " --> pdb=" O ASP 6 2 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE 6 26 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 6 35 " --> pdb=" O ALA 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 76 removed outlier: 3.972A pdb=" N PHE 6 50 " --> pdb=" O GLN 6 46 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix Processing helix chain '7' and resid 2 through 42 removed outlier: 3.826A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 77 removed outlier: 4.347A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix removed outlier: 3.841A pdb=" N ALA 7 63 " --> pdb=" O LEU 7 59 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 42 removed outlier: 3.532A pdb=" N ALA 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 78 removed outlier: 3.810A pdb=" N PHE 8 50 " --> pdb=" O GLN 8 46 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix Processing helix chain '9' and resid 2 through 42 removed outlier: 3.532A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 76 removed outlier: 4.384A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix removed outlier: 3.809A pdb=" N ASN 9 67 " --> pdb=" O ALA 9 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 51 removed outlier: 5.831A pdb=" N SER a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.773A pdb=" N ILE a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 128 through 151 removed outlier: 4.080A pdb=" N VAL a 132 " --> pdb=" O ASP a 128 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG a 151 " --> pdb=" O GLY a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 201 removed outlier: 4.103A pdb=" N GLU a 176 " --> pdb=" O ASN a 172 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL a 177 " --> pdb=" O LEU a 173 " (cutoff:3.500A) Proline residue: a 180 - end of helix removed outlier: 4.811A pdb=" N GLY a 194 " --> pdb=" O ASN a 190 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 204 No H-bonds generated for 'chain 'a' and resid 202 through 204' Processing helix chain 'a' and resid 209 through 243 removed outlier: 3.844A pdb=" N LEU a 221 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE a 222 " --> pdb=" O ALA a 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 643 hydrogen bonds defined for protein. 1929 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: 0.88 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2202 1.36 - 1.50: 2083 1.50 - 1.65: 2894 1.65 - 1.80: 9 1.80 - 1.94: 63 Bond restraints: 7251 Sorted by residual: bond pdb=" C11 UTI 6 600 " pdb=" O13 UTI 6 600 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C11 UTI 8 600 " pdb=" O13 UTI 8 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C11 UTI 5 600 " pdb=" O13 UTI 5 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C11 UTI 7 600 " pdb=" O13 UTI 7 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C11 UTI 9 600 " pdb=" O13 UTI 9 600 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 7246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 7839 1.78 - 3.56: 1725 3.56 - 5.34: 292 5.34 - 7.12: 20 7.12 - 8.91: 4 Bond angle restraints: 9880 Sorted by residual: angle pdb=" C MET 2 1 " pdb=" N ASP 2 2 " pdb=" CA ASP 2 2 " ideal model delta sigma weight residual 120.58 128.01 -7.43 1.32e+00 5.74e-01 3.17e+01 angle pdb=" C MET 7 1 " pdb=" N ASP 7 2 " pdb=" CA ASP 7 2 " ideal model delta sigma weight residual 120.09 126.64 -6.55 1.25e+00 6.40e-01 2.74e+01 angle pdb=" CA PHE 7 74 " pdb=" CB PHE 7 74 " pdb=" CG PHE 7 74 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.31e+01 angle pdb=" OE1 GLN 6 42 " pdb=" CD GLN 6 42 " pdb=" NE2 GLN 6 42 " ideal model delta sigma weight residual 122.60 117.83 4.77 1.00e+00 1.00e+00 2.27e+01 angle pdb=" OD1 ASN a 190 " pdb=" CG ASN a 190 " pdb=" ND2 ASN a 190 " ideal model delta sigma weight residual 122.60 117.96 4.64 1.00e+00 1.00e+00 2.15e+01 ... (remaining 9875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3796 17.85 - 35.71: 320 35.71 - 53.56: 57 53.56 - 71.42: 6 71.42 - 89.27: 6 Dihedral angle restraints: 4185 sinusoidal: 1613 harmonic: 2572 Sorted by residual: dihedral pdb=" CA ASP a 28 " pdb=" C ASP a 28 " pdb=" N THR a 29 " pdb=" CA THR a 29 " ideal model delta harmonic sigma weight residual 180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA HIS a 15 " pdb=" C HIS a 15 " pdb=" N HIS a 16 " pdb=" CA HIS a 16 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR a 27 " pdb=" C THR a 27 " pdb=" N ASP a 28 " pdb=" CA ASP a 28 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 858 0.084 - 0.169: 222 0.169 - 0.253: 45 0.253 - 0.337: 11 0.337 - 0.421: 1 Chirality restraints: 1137 Sorted by residual: chirality pdb=" C17 UTI a 600 " pdb=" C06 UTI a 600 " pdb=" C18 UTI a 600 " pdb=" C27 UTI a 600 " both_signs ideal model delta sigma weight residual False 2.42 2.84 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA ARG a 186 " pdb=" N ARG a 186 " pdb=" C ARG a 186 " pdb=" CB ARG a 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA PHE 9 54 " pdb=" N PHE 9 54 " pdb=" C PHE 9 54 " pdb=" CB PHE 9 54 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1134 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 64 " -0.097 2.00e-02 2.50e+03 5.33e-02 5.67e+01 pdb=" CG TYR 3 64 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 64 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 64 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 64 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR 3 64 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR 3 64 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 239 " 0.079 2.00e-02 2.50e+03 5.60e-02 5.48e+01 pdb=" CG PHE a 239 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE a 239 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE a 239 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE a 239 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE a 239 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE a 239 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 70 " -0.073 2.00e-02 2.50e+03 4.69e-02 3.84e+01 pdb=" CG PHE 5 70 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 70 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 70 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 70 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 70 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE 5 70 " -0.051 2.00e-02 2.50e+03 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 955 2.77 - 3.30: 7632 3.30 - 3.84: 11757 3.84 - 4.37: 14378 4.37 - 4.90: 24612 Nonbonded interactions: 59334 Sorted by model distance: nonbonded pdb=" OE2 GLU 5 61 " pdb=" N02 UTI 5 600 " model vdw 2.239 3.120 nonbonded pdb=" O THR 6 78 " pdb=" OG1 THR 6 78 " model vdw 2.328 3.040 nonbonded pdb=" O ALA 1 63 " pdb=" ND2 ASN 1 67 " model vdw 2.352 3.120 nonbonded pdb=" OE1 GLU 9 61 " pdb=" N02 UTI 9 600 " model vdw 2.391 3.120 nonbonded pdb=" ND2 ASN 4 33 " pdb=" O VAL 5 30 " model vdw 2.398 3.120 ... (remaining 59329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = (chain '4' and resid 1 through 81) selection = (chain '5' and resid 1 through 81) selection = (chain '6' and resid 1 through 81) selection = (chain '7' and resid 1 through 81) selection = (chain '8' and resid 1 through 81) selection = (chain '9' and resid 1 through 81) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.090 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.012 0.081 7251 Z= 0.652 Angle : 1.493 8.905 9880 Z= 1.006 Chirality : 0.081 0.421 1137 Planarity : 0.012 0.093 1228 Dihedral : 13.752 89.269 2565 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.23), residues: 925 helix: -1.39 (0.16), residues: 758 sheet: None (None), residues: 0 loop : -2.18 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 72 TYR 0.097 0.008 TYR 3 64 PHE 0.085 0.011 PHE a 239 TRP 0.046 0.005 TRP a 20 HIS 0.005 0.002 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.65 ( 7251) covalent geometry : angle 1.49337 / 1.01 ( 9880) hydrogen bonds : bond 0.18262 / 12.76 ( 643) hydrogen bonds : angle 8.94558 / 6.50 ( 1929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 52 THR cc_start: 0.4866 (p) cc_final: 0.4418 (m) REVERT: a 81 MET cc_start: 0.7094 (mmm) cc_final: 0.6843 (mtp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0602 time to fit residues: 16.6136 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 4 46 GLN 8 42 GLN ** a 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.173381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123989 restraints weight = 7669.916| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.85 r_work: 0.3450 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7251 Z= 0.174 Angle : 0.676 8.787 9880 Z= 0.345 Chirality : 0.045 0.195 1137 Planarity : 0.006 0.052 1228 Dihedral : 8.126 82.022 1214 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.08 % Allowed : 11.15 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 925 helix: 1.06 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.33 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 48 TYR 0.034 0.003 TYR a 143 PHE 0.017 0.001 PHE a 192 TRP 0.009 0.001 TRP a 216 HIS 0.002 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 7251) covalent geometry : angle 0.67608 / 0.34 ( 9880) hydrogen bonds : bond 0.04925 / 3.37 ( 643) hydrogen bonds : angle 4.66956 / 3.43 ( 1929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 61 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: 4 61 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8594 (mm-30) REVERT: 4 71 MET cc_start: 0.8561 (tmm) cc_final: 0.7993 (tmm) REVERT: a 61 GLN cc_start: 0.7230 (tp40) cc_final: 0.6296 (tt0) REVERT: a 81 MET cc_start: 0.7246 (mmm) cc_final: 0.7036 (mtp) outliers start: 7 outliers final: 4 residues processed: 155 average time/residue: 0.0618 time to fit residues: 13.6443 Evaluate side-chains 134 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 70 GLN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123341 restraints weight = 7651.255| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.84 r_work: 0.3442 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7251 Z= 0.168 Angle : 0.651 8.375 9880 Z= 0.321 Chirality : 0.044 0.189 1137 Planarity : 0.005 0.050 1228 Dihedral : 7.116 71.874 1214 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 13.00 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.28), residues: 925 helix: 1.95 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.48 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.033 0.002 TYR a 143 PHE 0.026 0.001 PHE a 138 TRP 0.007 0.001 TRP a 103 HIS 0.002 0.001 HIS a 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 7251) covalent geometry : angle 0.65113 / 0.32 ( 9880) hydrogen bonds : bond 0.04525 / 3.06 ( 643) hydrogen bonds : angle 4.39209 / 3.24 ( 1929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: 1 73 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (tp) REVERT: 3 61 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: 4 71 MET cc_start: 0.8505 (tmm) cc_final: 0.7759 (tmm) REVERT: 5 71 MET cc_start: 0.8573 (tmm) cc_final: 0.8305 (tmm) REVERT: 8 42 GLN cc_start: 0.8004 (mt0) cc_final: 0.7547 (mt0) REVERT: 8 54 PHE cc_start: 0.8437 (m-80) cc_final: 0.8208 (m-80) REVERT: a 61 GLN cc_start: 0.7199 (tp40) cc_final: 0.6266 (tt0) REVERT: a 81 MET cc_start: 0.7237 (mmm) cc_final: 0.6965 (mtp) REVERT: a 104 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6849 (mt) REVERT: a 179 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7961 (mttt) REVERT: a 238 TYR cc_start: 0.8067 (m-10) cc_final: 0.7734 (m-80) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.0670 time to fit residues: 13.5701 Evaluate side-chains 140 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 5 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.2038 > 50:) chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120992 restraints weight = 7647.463| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.84 r_work: 0.3431 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7251 Z= 0.170 Angle : 0.643 8.185 9880 Z= 0.317 Chirality : 0.044 0.203 1137 Planarity : 0.005 0.053 1228 Dihedral : 6.372 53.455 1214 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.48 % Allowed : 14.24 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.28), residues: 925 helix: 2.16 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.60 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 6 48 TYR 0.025 0.002 TYR a 143 PHE 0.018 0.001 PHE a 64 TRP 0.007 0.001 TRP a 216 HIS 0.005 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 7251) covalent geometry : angle 0.64258 / 0.32 ( 9880) hydrogen bonds : bond 0.04397 / 2.96 ( 643) hydrogen bonds : angle 4.29632 / 3.17 ( 1929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: 3 61 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: 8 42 GLN cc_start: 0.7917 (mt0) cc_final: 0.7713 (mt0) REVERT: 8 46 GLN cc_start: 0.8216 (tt0) cc_final: 0.7984 (tt0) REVERT: 9 80 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (m) REVERT: a 11 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6501 (mm-30) REVERT: a 61 GLN cc_start: 0.7257 (tp40) cc_final: 0.6331 (tt0) REVERT: a 81 MET cc_start: 0.7237 (mmm) cc_final: 0.6941 (mtp) REVERT: a 104 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6744 (mt) REVERT: a 188 PHE cc_start: 0.7519 (t80) cc_final: 0.7277 (t80) outliers start: 16 outliers final: 6 residues processed: 142 average time/residue: 0.0683 time to fit residues: 13.5347 Evaluate side-chains 135 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124650 restraints weight = 7734.758| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.82 r_work: 0.3489 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7251 Z= 0.145 Angle : 0.621 8.774 9880 Z= 0.305 Chirality : 0.043 0.189 1137 Planarity : 0.005 0.052 1228 Dihedral : 5.693 38.094 1214 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 15.63 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.28), residues: 925 helix: 2.43 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.026 0.002 TYR a 238 PHE 0.012 0.001 PHE a 63 TRP 0.009 0.001 TRP a 216 HIS 0.009 0.002 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 7251) covalent geometry : angle 0.62134 / 0.31 ( 9880) hydrogen bonds : bond 0.04175 / 2.81 ( 643) hydrogen bonds : angle 4.17573 / 3.08 ( 1929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.235 Fit side-chains REVERT: 2 80 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8656 (m) REVERT: 3 61 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: 6 1 MET cc_start: 0.2892 (mmp) cc_final: 0.2604 (mmp) REVERT: 8 46 GLN cc_start: 0.8184 (tt0) cc_final: 0.7964 (tt0) REVERT: 9 80 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8153 (m) REVERT: a 11 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6459 (mm-30) REVERT: a 61 GLN cc_start: 0.7180 (tp40) cc_final: 0.6309 (tt0) REVERT: a 70 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7769 (tp-100) REVERT: a 81 MET cc_start: 0.7321 (mmm) cc_final: 0.6927 (mtp) REVERT: a 104 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6594 (mt) outliers start: 14 outliers final: 8 residues processed: 138 average time/residue: 0.0678 time to fit residues: 13.1333 Evaluate side-chains 131 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 80 VAL Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 42 GLN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.175040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125395 restraints weight = 7887.486| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.83 r_work: 0.3490 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7251 Z= 0.146 Angle : 0.627 8.994 9880 Z= 0.308 Chirality : 0.044 0.190 1137 Planarity : 0.005 0.052 1228 Dihedral : 5.546 38.330 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 16.25 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.28), residues: 925 helix: 2.55 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.71 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 48 TYR 0.024 0.002 TYR a 143 PHE 0.026 0.001 PHE a 188 TRP 0.007 0.001 TRP a 216 HIS 0.002 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 7251) covalent geometry : angle 0.62722 / 0.31 ( 9880) hydrogen bonds : bond 0.04112 / 2.76 ( 643) hydrogen bonds : angle 4.17698 / 3.08 ( 1929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.235 Fit side-chains REVERT: 2 80 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8620 (m) REVERT: 3 61 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: 5 73 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.6950 (mp) REVERT: 6 1 MET cc_start: 0.2819 (mmp) cc_final: 0.2584 (mmp) REVERT: 7 71 MET cc_start: 0.8921 (tmm) cc_final: 0.8712 (tmt) REVERT: 8 46 GLN cc_start: 0.8160 (tt0) cc_final: 0.7940 (tt0) REVERT: 9 80 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8183 (m) REVERT: a 61 GLN cc_start: 0.7198 (tp40) cc_final: 0.6345 (tt0) REVERT: a 70 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7763 (tp-100) REVERT: a 81 MET cc_start: 0.7323 (mmm) cc_final: 0.6905 (mtp) REVERT: a 104 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6590 (mt) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.0667 time to fit residues: 12.6944 Evaluate side-chains 134 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 80 VAL Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 227 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 28 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.174173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124098 restraints weight = 7764.933| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.81 r_work: 0.3486 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7251 Z= 0.156 Angle : 0.635 9.213 9880 Z= 0.313 Chirality : 0.044 0.187 1137 Planarity : 0.005 0.051 1228 Dihedral : 5.532 38.016 1214 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.63 % Allowed : 17.49 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.28), residues: 925 helix: 2.51 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.70 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 48 TYR 0.030 0.002 TYR a 238 PHE 0.023 0.001 PHE a 140 TRP 0.006 0.001 TRP a 216 HIS 0.016 0.003 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 7251) covalent geometry : angle 0.63461 / 0.31 ( 9880) hydrogen bonds : bond 0.04207 / 2.81 ( 643) hydrogen bonds : angle 4.21355 / 3.11 ( 1929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.186 Fit side-chains REVERT: 2 80 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8612 (m) REVERT: 3 61 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: 5 73 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.6906 (mp) REVERT: 6 1 MET cc_start: 0.2579 (mmp) cc_final: 0.2298 (mmp) REVERT: 9 80 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8155 (m) REVERT: a 61 GLN cc_start: 0.7172 (tp40) cc_final: 0.6313 (tt0) REVERT: a 70 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7754 (tp-100) REVERT: a 81 MET cc_start: 0.7287 (mmm) cc_final: 0.7007 (mtp) REVERT: a 104 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6562 (mt) outliers start: 17 outliers final: 9 residues processed: 135 average time/residue: 0.0745 time to fit residues: 14.0211 Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 2 residue 80 VAL Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 239 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 42 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.171185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121813 restraints weight = 7746.814| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.78 r_work: 0.3484 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7251 Z= 0.183 Angle : 0.667 9.386 9880 Z= 0.330 Chirality : 0.045 0.208 1137 Planarity : 0.005 0.052 1228 Dihedral : 5.687 38.028 1214 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.79 % Allowed : 17.96 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.28), residues: 925 helix: 2.42 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.034 0.002 TYR a 238 PHE 0.019 0.001 PHE a 138 TRP 0.007 0.001 TRP a 103 HIS 0.004 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 7251) covalent geometry : angle 0.66669 / 0.33 ( 9880) hydrogen bonds : bond 0.04385 / 2.93 ( 643) hydrogen bonds : angle 4.30074 / 3.18 ( 1929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: 3 61 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: 5 1 MET cc_start: 0.5980 (ptp) cc_final: 0.5553 (ptm) REVERT: 6 1 MET cc_start: 0.2648 (mmp) cc_final: 0.2377 (mmp) REVERT: 7 71 MET cc_start: 0.8975 (tmm) cc_final: 0.8744 (tmt) REVERT: 9 1 MET cc_start: 0.7662 (tpp) cc_final: 0.7441 (tpp) REVERT: 9 80 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (m) REVERT: a 61 GLN cc_start: 0.7166 (tp40) cc_final: 0.6315 (tt0) REVERT: a 70 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7770 (tp-100) REVERT: a 104 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6524 (mt) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 0.0680 time to fit residues: 12.3965 Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 8 residue 80 VAL Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 227 GLN Chi-restraints excluded: chain a residue 239 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124244 restraints weight = 7627.817| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.77 r_work: 0.3488 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7251 Z= 0.155 Angle : 0.662 9.721 9880 Z= 0.325 Chirality : 0.045 0.185 1137 Planarity : 0.005 0.050 1228 Dihedral : 5.555 37.410 1214 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.48 % Allowed : 18.11 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.28), residues: 925 helix: 2.53 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.77 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 48 TYR 0.035 0.002 TYR a 238 PHE 0.023 0.001 PHE 6 70 TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 7251) covalent geometry : angle 0.66180 / 0.33 ( 9880) hydrogen bonds : bond 0.04219 / 2.81 ( 643) hydrogen bonds : angle 4.23547 / 3.13 ( 1929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: 3 61 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: 5 1 MET cc_start: 0.5962 (ptp) cc_final: 0.5488 (ptm) REVERT: 5 73 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.6979 (mp) REVERT: 6 1 MET cc_start: 0.2496 (mmp) cc_final: 0.2234 (mmp) REVERT: 7 71 MET cc_start: 0.8938 (tmm) cc_final: 0.8699 (tmt) REVERT: 9 1 MET cc_start: 0.7600 (tpp) cc_final: 0.7387 (tpp) REVERT: 9 80 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (m) REVERT: a 61 GLN cc_start: 0.7086 (tp40) cc_final: 0.6246 (tt0) REVERT: a 104 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6470 (tp) REVERT: a 243 MET cc_start: 0.6280 (tpt) cc_final: 0.4489 (mtt) outliers start: 16 outliers final: 12 residues processed: 126 average time/residue: 0.0718 time to fit residues: 12.5333 Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 8 residue 80 VAL Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 227 GLN Chi-restraints excluded: chain a residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 70 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120758 restraints weight = 7680.484| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.83 r_work: 0.3456 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7251 Z= 0.179 Angle : 0.682 9.655 9880 Z= 0.335 Chirality : 0.045 0.203 1137 Planarity : 0.005 0.059 1228 Dihedral : 5.709 37.362 1214 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.79 % Allowed : 17.80 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.28), residues: 925 helix: 2.43 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.037 0.003 TYR a 238 PHE 0.016 0.001 PHE 7 70 TRP 0.007 0.001 TRP a 103 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 7251) covalent geometry : angle 0.68173 / 0.33 ( 9880) hydrogen bonds : bond 0.04360 / 2.91 ( 643) hydrogen bonds : angle 4.29645 / 3.17 ( 1929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.243 Fit side-chains REVERT: 3 61 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: 5 1 MET cc_start: 0.5872 (ptp) cc_final: 0.5394 (ptm) REVERT: 6 1 MET cc_start: 0.2484 (mmp) cc_final: 0.2213 (mmp) REVERT: 7 71 MET cc_start: 0.8942 (tmm) cc_final: 0.8670 (tmt) REVERT: 9 1 MET cc_start: 0.7607 (tpp) cc_final: 0.7402 (tpp) REVERT: 9 80 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8166 (m) REVERT: a 61 GLN cc_start: 0.7074 (tp40) cc_final: 0.6225 (tt0) REVERT: a 104 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6463 (tp) REVERT: a 243 MET cc_start: 0.6336 (tpt) cc_final: 0.4476 (mtt) outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 0.0762 time to fit residues: 13.6866 Evaluate side-chains 133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 42 GLN Chi-restraints excluded: chain 5 residue 73 LEU Chi-restraints excluded: chain 8 residue 57 VAL Chi-restraints excluded: chain 9 residue 68 LEU Chi-restraints excluded: chain 9 residue 80 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 90 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 227 GLN Chi-restraints excluded: chain a residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.174443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123121 restraints weight = 7663.545| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.83 r_work: 0.3492 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7251 Z= 0.150 Angle : 0.664 9.512 9880 Z= 0.324 Chirality : 0.044 0.187 1137 Planarity : 0.005 0.051 1228 Dihedral : 5.559 37.073 1214 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.17 % Allowed : 18.58 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.28), residues: 925 helix: 2.59 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 72 TYR 0.035 0.002 TYR a 238 PHE 0.016 0.001 PHE a 188 TRP 0.007 0.001 TRP a 216 HIS 0.002 0.001 HIS a 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 7251) covalent geometry : angle 0.66388 / 0.32 ( 9880) hydrogen bonds : bond 0.04149 / 2.76 ( 643) hydrogen bonds : angle 4.21133 / 3.11 ( 1929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.39 seconds wall clock time: 35 minutes 56.19 seconds (2156.19 seconds total)