Starting phenix.real_space_refine on Fri Jul 3 20:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pke_13469/07_2026/7pke_13469.map" } resolution = 3.3 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= 0.002 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: 7 Type Number sf(0) Gaussians Ca 10 9.91 5 P 5 5.49 5 S 20 5.16 5 C 5315 2.51 5 N 1310 2.21 5 O 1570 1.98 5 H 7970 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16200 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.17 Number of scatterers: 16200 At special positions: 0 Unit cell: (112.86, 114.532, 53.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 10 19.99 S 20 16.00 P 5 15.00 O 1570 8.00 N 1310 7.00 C 5315 6.00 H 7970 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 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: 1.01 Conformation dependent library (CDL) restraints added in 327.8 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 15 sheets defined 12.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.986A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 176 removed outlier: 3.743A pdb=" N THR E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.181A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.914A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 186 through 190 removed outlier: 4.159A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.974A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 186 through 190 removed outlier: 4.000A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.965A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 186 through 190 removed outlier: 4.090A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.865A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 186 through 190 removed outlier: 4.007A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.743A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 85 removed outlier: 6.254A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.755A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.088A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.775A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.206A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.774A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.196A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.842A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 80 through 85 removed outlier: 4.530A pdb=" N ASN A 61 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR A 54 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 63 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 52 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 65 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 50 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7970 1.03 - 1.22: 1 1.22 - 1.42: 3643 1.42 - 1.61: 4766 1.61 - 1.80: 30 Bond restraints: 16410 Sorted by residual: bond pdb=" O2 PC A 303 " pdb=" P1 PC A 303 " ideal model delta sigma weight residual 1.733 1.603 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" O2 PC E 303 " pdb=" P1 PC E 303 " ideal model delta sigma weight residual 1.733 1.604 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" O2 PC D 303 " pdb=" P1 PC D 303 " ideal model delta sigma weight residual 1.733 1.604 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" O2 PC B 303 " pdb=" P1 PC B 303 " ideal model delta sigma weight residual 1.733 1.605 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" O2 PC C 303 " pdb=" P1 PC C 303 " ideal model delta sigma weight residual 1.733 1.606 0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 16405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 29536 5.94 - 11.89: 46 11.89 - 17.83: 1 17.83 - 23.77: 4 23.77 - 29.72: 23 Bond angle restraints: 29610 Sorted by residual: angle pdb=" CG2 VAL E 77 " pdb=" CB VAL E 77 " pdb=" HB VAL E 77 " ideal model delta sigma weight residual 108.00 78.28 29.72 3.00e+00 1.11e-01 9.81e+01 angle pdb=" CG2 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 108.00 79.35 28.65 3.00e+00 1.11e-01 9.12e+01 angle pdb=" OG1 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 109.00 80.70 28.30 3.00e+00 1.11e-01 8.90e+01 angle pdb=" CG1 VAL E 77 " pdb=" CB VAL E 77 " pdb=" HB VAL E 77 " ideal model delta sigma weight residual 108.00 80.46 27.54 3.00e+00 1.11e-01 8.43e+01 angle pdb=" CA THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 109.00 81.58 27.42 3.00e+00 1.11e-01 8.35e+01 ... (remaining 29605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 7011 16.69 - 33.39: 489 33.39 - 50.08: 159 50.08 - 66.78: 140 66.78 - 83.47: 16 Dihedral angle restraints: 7815 sinusoidal: 4140 harmonic: 3675 Sorted by residual: dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLU D 62 " pdb=" C GLU D 62 " pdb=" N ILE D 63 " pdb=" CA ILE D 63 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 7812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 1226 0.344 - 0.688: 0 0.688 - 1.032: 0 1.032 - 1.377: 4 1.377 - 1.721: 5 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CB VAL B 89 " pdb=" CA VAL B 89 " pdb=" CG1 VAL B 89 " pdb=" CG2 VAL B 89 " both_signs ideal model delta sigma weight residual False -2.63 -1.04 -1.59 2.00e-01 2.50e+01 6.29e+01 chirality pdb=" CB ILE A 82 " pdb=" CA ILE A 82 " pdb=" CG1 ILE A 82 " pdb=" CG2 ILE A 82 " both_signs ideal model delta sigma weight residual False 2.64 1.06 1.58 2.00e-01 2.50e+01 6.24e+01 ... (remaining 1232 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 150 " -0.040 2.00e-02 2.50e+03 4.90e-02 3.60e+01 pdb=" CD GLN E 150 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN E 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN E 150 " 0.077 2.00e-02 2.50e+03 pdb="HE21 GLN E 150 " 0.002 2.00e-02 2.50e+03 pdb="HE22 GLN E 150 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 150 " -0.037 2.00e-02 2.50e+03 4.37e-02 2.86e+01 pdb=" CD GLN C 150 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN C 150 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN C 150 " 0.067 2.00e-02 2.50e+03 pdb="HE21 GLN C 150 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN C 150 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 150 " -0.033 2.00e-02 2.50e+03 3.96e-02 2.35e+01 pdb=" CD GLN D 150 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN D 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN D 150 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN D 150 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN D 150 " -0.060 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 607 2.14 - 2.76: 30498 2.76 - 3.37: 45049 3.37 - 3.99: 62704 3.99 - 4.60: 96631 Nonbonded interactions: 235489 Sorted by model distance: nonbonded pdb=" OD1 ASP E 163 " pdb="HD22 ASN E 183 " model vdw 1.529 2.450 nonbonded pdb=" OD1 ASP D 163 " pdb="HD22 ASN D 183 " model vdw 1.546 2.450 nonbonded pdb=" OD2 ASP A 163 " pdb="HD22 ASN A 183 " model vdw 1.594 2.450 nonbonded pdb=" HG SER A 141 " pdb=" OD1 ASN A 145 " model vdw 1.623 2.450 nonbonded pdb=" HG SER D 102 " pdb=" O TYR D 125 " model vdw 1.624 2.450 ... (remaining 235484 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.810 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: 0.100 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 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 : 0.008 0.130 8445 Z= 0.374 Angle : 0.930 14.288 11490 Z= 0.478 Chirality : 0.132 1.721 1235 Planarity : 0.006 0.115 1450 Dihedral : 13.263 83.470 3030 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.25), residues: 1020 helix: 0.69 (0.69), residues: 50 sheet: -0.06 (0.24), residues: 425 loop : -0.51 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.009 ARG C 118 TYR 0.023 0.006 TYR B 54 PHE 0.023 0.003 PHE D 66 TRP 0.022 0.005 TRP A 187 HIS 0.006 0.003 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.37 ( 8440) covalent geometry : angle 0.93004 / 0.48 (11480) SS BOND : bond 0.00128 / 0.06 ( 5) SS BOND : angle 0.41606 / 0.24 ( 10) hydrogen bonds : bond 0.19133 / 12.33 ( 327) hydrogen bonds : angle 8.19120 / 5.52 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8133 (p0) cc_final: 0.7692 (p0) REVERT: D 188 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: B 16 ASP cc_start: 0.8290 (p0) cc_final: 0.7899 (p0) REVERT: A 16 ASP cc_start: 0.8147 (p0) cc_final: 0.7831 (p0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2479 time to fit residues: 33.6605 Evaluate side-chains 88 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 HIS E 95 HIS E 172 ASN D 38 HIS D 95 HIS D 195 GLN C 38 HIS C 95 HIS B 38 HIS B 59 GLN B 95 HIS A 38 HIS A 95 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.073973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.060328 restraints weight = 37667.822| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 2.17 r_work: 0.2326 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2186 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8445 Z= 0.143 Angle : 0.711 15.338 11490 Z= 0.378 Chirality : 0.133 1.675 1235 Planarity : 0.005 0.064 1450 Dihedral : 7.188 59.579 1140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.67 % Allowed : 3.22 % Favored : 96.11 % 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: 0.15 (0.26), residues: 1020 helix: 2.24 (0.69), residues: 55 sheet: 0.39 (0.24), residues: 415 loop : -0.29 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 188 TYR 0.025 0.001 TYR E 54 PHE 0.015 0.001 PHE E 66 TRP 0.009 0.001 TRP C 110 HIS 0.004 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8440) covalent geometry : angle 0.71152 / 0.38 (11480) SS BOND : bond 0.00185 / 0.10 ( 5) SS BOND : angle 0.58312 / 0.35 ( 10) hydrogen bonds : bond 0.04727 / 3.05 ( 327) hydrogen bonds : angle 5.95897 / 3.97 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: D 188 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8500 (mtm-85) REVERT: C 28 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7921 (ttpt) REVERT: B 16 ASP cc_start: 0.8540 (p0) cc_final: 0.8042 (p0) REVERT: B 59 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8467 (tp-100) REVERT: A 16 ASP cc_start: 0.8447 (p0) cc_final: 0.8074 (p0) REVERT: A 140 ASP cc_start: 0.8885 (m-30) cc_final: 0.8603 (m-30) REVERT: A 188 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8420 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 109 average time/residue: 0.2662 time to fit residues: 36.8064 Evaluate side-chains 92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain A residue 38 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS C 38 HIS B 38 HIS A 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.073163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.059932 restraints weight = 38539.476| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 2.17 r_work: 0.2323 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2187 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8445 Z= 0.153 Angle : 0.674 15.672 11490 Z= 0.357 Chirality : 0.133 1.688 1235 Planarity : 0.004 0.040 1450 Dihedral : 6.245 44.046 1140 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.56 % Allowed : 4.11 % Favored : 95.33 % 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: 0.04 (0.25), residues: 1020 helix: 2.33 (0.63), residues: 55 sheet: 0.33 (0.22), residues: 445 loop : -0.44 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 6 TYR 0.021 0.001 TYR E 54 PHE 0.010 0.001 PHE B 66 TRP 0.008 0.001 TRP A 162 HIS 0.011 0.006 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 8440) covalent geometry : angle 0.67380 / 0.36 (11480) SS BOND : bond 0.00086 / 0.05 ( 5) SS BOND : angle 0.60749 / 0.38 ( 10) hydrogen bonds : bond 0.04344 / 2.78 ( 327) hydrogen bonds : angle 5.64857 / 3.77 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: E 125 TYR cc_start: 0.8862 (t80) cc_final: 0.8456 (t80) REVERT: D 163 ASP cc_start: 0.8627 (p0) cc_final: 0.8332 (p0) REVERT: D 188 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8439 (mtm-85) REVERT: B 16 ASP cc_start: 0.8549 (p0) cc_final: 0.8030 (p0) REVERT: B 59 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8401 (tp-100) REVERT: B 163 ASP cc_start: 0.8678 (p0) cc_final: 0.8242 (p0) outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.2460 time to fit residues: 30.3430 Evaluate side-chains 92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.069651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.056397 restraints weight = 38740.752| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 2.16 r_work: 0.2338 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2200 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 8445 Z= 0.276 Angle : 0.701 15.895 11490 Z= 0.372 Chirality : 0.134 1.691 1235 Planarity : 0.004 0.030 1450 Dihedral : 6.195 34.103 1140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.56 % Allowed : 6.11 % Favored : 93.33 % 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: -0.19 (0.25), residues: 1020 helix: 2.08 (0.61), residues: 55 sheet: 0.21 (0.23), residues: 445 loop : -0.62 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 118 TYR 0.024 0.002 TYR E 54 PHE 0.012 0.002 PHE D 52 TRP 0.011 0.001 TRP E 162 HIS 0.010 0.003 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 ( 8440) covalent geometry : angle 0.70077 / 0.37 (11480) SS BOND : bond 0.00111 / 0.06 ( 5) SS BOND : angle 0.35938 / 0.23 ( 10) hydrogen bonds : bond 0.04507 / 2.89 ( 327) hydrogen bonds : angle 5.56103 / 3.72 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.449 Fit side-chains REVERT: E 28 LYS cc_start: 0.8254 (ttpt) cc_final: 0.8052 (ttpt) REVERT: D 16 ASP cc_start: 0.8628 (p0) cc_final: 0.8241 (p0) REVERT: B 16 ASP cc_start: 0.8650 (p0) cc_final: 0.8162 (p0) REVERT: B 125 TYR cc_start: 0.8943 (t80) cc_final: 0.8694 (t80) REVERT: B 163 ASP cc_start: 0.8720 (p0) cc_final: 0.8229 (p0) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.2665 time to fit residues: 33.3623 Evaluate side-chains 94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.071660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.058157 restraints weight = 38225.946| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 2.19 r_work: 0.2351 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8445 Z= 0.161 Angle : 0.655 15.770 11490 Z= 0.344 Chirality : 0.133 1.689 1235 Planarity : 0.004 0.052 1450 Dihedral : 5.799 28.432 1140 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.44 % Allowed : 7.22 % Favored : 92.33 % 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: -0.19 (0.25), residues: 1020 helix: 2.02 (0.57), residues: 55 sheet: 0.17 (0.23), residues: 445 loop : -0.57 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 188 TYR 0.017 0.001 TYR E 54 PHE 0.010 0.001 PHE B 66 TRP 0.007 0.001 TRP B 110 HIS 0.006 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8440) covalent geometry : angle 0.65506 / 0.34 (11480) SS BOND : bond 0.00151 / 0.08 ( 5) SS BOND : angle 0.39422 / 0.27 ( 10) hydrogen bonds : bond 0.03795 / 2.42 ( 327) hydrogen bonds : angle 5.44616 / 3.64 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.460 Fit side-chains REVERT: D 16 ASP cc_start: 0.8595 (p0) cc_final: 0.8201 (p0) REVERT: C 163 ASP cc_start: 0.8716 (p0) cc_final: 0.8455 (p0) REVERT: C 188 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8292 (mtt90) REVERT: B 16 ASP cc_start: 0.8600 (p0) cc_final: 0.8122 (p0) REVERT: B 125 TYR cc_start: 0.8891 (t80) cc_final: 0.8614 (t80) REVERT: B 163 ASP cc_start: 0.8703 (p0) cc_final: 0.8235 (p0) outliers start: 4 outliers final: 4 residues processed: 102 average time/residue: 0.2442 time to fit residues: 32.0948 Evaluate side-chains 96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.072217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.058780 restraints weight = 38010.002| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.19 r_work: 0.2385 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2246 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8445 Z= 0.151 Angle : 0.643 15.731 11490 Z= 0.337 Chirality : 0.133 1.687 1235 Planarity : 0.004 0.054 1450 Dihedral : 5.584 33.503 1140 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.78 % Allowed : 7.67 % Favored : 91.56 % 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: -0.08 (0.25), residues: 1020 helix: 1.92 (0.57), residues: 55 sheet: 0.34 (0.24), residues: 415 loop : -0.53 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 188 TYR 0.017 0.001 TYR E 54 PHE 0.009 0.001 PHE E 52 TRP 0.006 0.001 TRP B 110 HIS 0.006 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 8440) covalent geometry : angle 0.64314 / 0.34 (11480) SS BOND : bond 0.00151 / 0.09 ( 5) SS BOND : angle 0.36212 / 0.24 ( 10) hydrogen bonds : bond 0.03606 / 2.30 ( 327) hydrogen bonds : angle 5.36654 / 3.58 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.533 Fit side-chains REVERT: D 13 LYS cc_start: 0.8767 (mttt) cc_final: 0.8542 (mmtt) REVERT: D 16 ASP cc_start: 0.8583 (p0) cc_final: 0.8201 (p0) REVERT: D 163 ASP cc_start: 0.8673 (p0) cc_final: 0.8464 (p0) REVERT: C 163 ASP cc_start: 0.8710 (p0) cc_final: 0.8474 (p0) REVERT: C 188 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8286 (mtt90) REVERT: B 125 TYR cc_start: 0.8911 (t80) cc_final: 0.8640 (t80) REVERT: B 163 ASP cc_start: 0.8658 (p0) cc_final: 0.8245 (p0) REVERT: A 163 ASP cc_start: 0.8534 (p0) cc_final: 0.8293 (p0) outliers start: 7 outliers final: 4 residues processed: 109 average time/residue: 0.2525 time to fit residues: 35.7648 Evaluate side-chains 100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.072898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.059637 restraints weight = 38002.517| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 2.13 r_work: 0.2295 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2160 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8445 Z= 0.150 Angle : 0.642 15.733 11490 Z= 0.337 Chirality : 0.133 1.689 1235 Planarity : 0.004 0.058 1450 Dihedral : 5.479 40.699 1140 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.33 % 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: -0.10 (0.25), residues: 1020 helix: 1.94 (0.57), residues: 55 sheet: 0.34 (0.24), residues: 415 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 188 TYR 0.015 0.001 TYR E 54 PHE 0.010 0.001 PHE E 52 TRP 0.006 0.001 TRP D 110 HIS 0.005 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 8440) covalent geometry : angle 0.64227 / 0.34 (11480) SS BOND : bond 0.00142 / 0.08 ( 5) SS BOND : angle 0.37722 / 0.26 ( 10) hydrogen bonds : bond 0.03559 / 2.26 ( 327) hydrogen bonds : angle 5.31912 / 3.55 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.400 Fit side-chains REVERT: E 1 GLN cc_start: 0.8271 (mp10) cc_final: 0.7886 (mm-40) REVERT: D 13 LYS cc_start: 0.8720 (mttt) cc_final: 0.8455 (mmtt) REVERT: D 16 ASP cc_start: 0.8585 (p0) cc_final: 0.8187 (p0) REVERT: D 163 ASP cc_start: 0.8597 (p0) cc_final: 0.8382 (p0) REVERT: C 163 ASP cc_start: 0.8652 (p0) cc_final: 0.8360 (p0) REVERT: C 188 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8266 (mtt90) REVERT: B 125 TYR cc_start: 0.8863 (t80) cc_final: 0.8570 (t80) REVERT: B 163 ASP cc_start: 0.8623 (p0) cc_final: 0.8151 (p0) REVERT: A 163 ASP cc_start: 0.8506 (p0) cc_final: 0.8242 (p0) outliers start: 6 outliers final: 4 residues processed: 109 average time/residue: 0.2385 time to fit residues: 33.5198 Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 29 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.073422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.059995 restraints weight = 38018.750| |-----------------------------------------------------------------------------| r_work (start): 0.2403 rms_B_bonded: 2.19 r_work: 0.2295 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2161 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8445 Z= 0.121 Angle : 0.630 15.699 11490 Z= 0.329 Chirality : 0.133 1.691 1235 Planarity : 0.004 0.059 1450 Dihedral : 5.276 43.935 1140 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.33 % 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: -0.05 (0.26), residues: 1020 helix: 1.98 (0.57), residues: 55 sheet: 0.36 (0.24), residues: 415 loop : -0.51 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 188 TYR 0.014 0.001 TYR E 54 PHE 0.009 0.001 PHE A 52 TRP 0.006 0.001 TRP D 110 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 8440) covalent geometry : angle 0.63008 / 0.33 (11480) SS BOND : bond 0.00159 / 0.09 ( 5) SS BOND : angle 0.39173 / 0.27 ( 10) hydrogen bonds : bond 0.03325 / 2.10 ( 327) hydrogen bonds : angle 5.27574 / 3.52 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.425 Fit side-chains REVERT: E 1 GLN cc_start: 0.8282 (mp10) cc_final: 0.7992 (mm110) REVERT: D 13 LYS cc_start: 0.8731 (mttt) cc_final: 0.8497 (mmtt) REVERT: D 16 ASP cc_start: 0.8593 (p0) cc_final: 0.8208 (p0) REVERT: D 188 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8410 (mtt90) REVERT: C 188 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8333 (mtt90) REVERT: B 125 TYR cc_start: 0.8877 (t80) cc_final: 0.8588 (t80) REVERT: B 163 ASP cc_start: 0.8610 (p0) cc_final: 0.8166 (p0) REVERT: A 163 ASP cc_start: 0.8509 (p0) cc_final: 0.8275 (p0) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.2231 time to fit residues: 31.9674 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.073188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.059827 restraints weight = 37975.974| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 2.19 r_work: 0.2294 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2159 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8445 Z= 0.130 Angle : 0.632 15.700 11490 Z= 0.330 Chirality : 0.133 1.698 1235 Planarity : 0.004 0.051 1450 Dihedral : 5.285 49.264 1140 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.56 % Allowed : 8.22 % Favored : 91.22 % 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: -0.04 (0.26), residues: 1020 helix: 2.07 (0.57), residues: 55 sheet: 0.38 (0.25), residues: 415 loop : -0.53 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 188 TYR 0.014 0.001 TYR E 54 PHE 0.009 0.001 PHE E 52 TRP 0.006 0.001 TRP B 162 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8440) covalent geometry : angle 0.63265 / 0.33 (11480) SS BOND : bond 0.00157 / 0.09 ( 5) SS BOND : angle 0.38048 / 0.25 ( 10) hydrogen bonds : bond 0.03374 / 2.13 ( 327) hydrogen bonds : angle 5.25656 / 3.52 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8729 (mttt) cc_final: 0.8497 (mmtt) REVERT: D 16 ASP cc_start: 0.8588 (p0) cc_final: 0.8194 (p0) REVERT: D 188 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8420 (mtt90) REVERT: C 188 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8343 (mtt90) REVERT: B 125 TYR cc_start: 0.8900 (t80) cc_final: 0.8608 (t80) REVERT: B 163 ASP cc_start: 0.8594 (p0) cc_final: 0.8163 (p0) REVERT: A 163 ASP cc_start: 0.8537 (p0) cc_final: 0.8308 (p0) outliers start: 5 outliers final: 4 residues processed: 112 average time/residue: 0.2316 time to fit residues: 33.3767 Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN A 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.072383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.059033 restraints weight = 37950.184| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 2.18 r_work: 0.2279 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2144 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8445 Z= 0.160 Angle : 0.642 15.753 11490 Z= 0.336 Chirality : 0.134 1.703 1235 Planarity : 0.004 0.050 1450 Dihedral : 5.422 54.594 1140 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.56 % Allowed : 8.56 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.26), residues: 1020 helix: 2.10 (0.58), residues: 55 sheet: 0.37 (0.25), residues: 415 loop : -0.58 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 188 TYR 0.014 0.001 TYR E 54 PHE 0.010 0.001 PHE E 52 TRP 0.007 0.001 TRP B 162 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 8440) covalent geometry : angle 0.64206 / 0.34 (11480) SS BOND : bond 0.00148 / 0.08 ( 5) SS BOND : angle 0.33225 / 0.22 ( 10) hydrogen bonds : bond 0.03508 / 2.21 ( 327) hydrogen bonds : angle 5.27155 / 3.53 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8722 (mttt) cc_final: 0.8479 (mmtt) REVERT: D 16 ASP cc_start: 0.8581 (p0) cc_final: 0.8189 (p0) REVERT: D 188 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8412 (mtt90) REVERT: C 1 GLN cc_start: 0.7935 (mm110) cc_final: 0.7481 (mm110) REVERT: C 188 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8349 (mtt90) REVERT: B 125 TYR cc_start: 0.8904 (t80) cc_final: 0.8606 (t80) REVERT: B 163 ASP cc_start: 0.8592 (p0) cc_final: 0.8149 (p0) REVERT: A 85 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8447 (mm-30) REVERT: A 163 ASP cc_start: 0.8553 (p0) cc_final: 0.8315 (p0) outliers start: 5 outliers final: 4 residues processed: 109 average time/residue: 0.2341 time to fit residues: 32.5592 Evaluate side-chains 109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.072704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.059261 restraints weight = 37806.942| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.19 r_work: 0.2395 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2256 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8445 Z= 0.148 Angle : 0.638 15.742 11490 Z= 0.333 Chirality : 0.133 1.703 1235 Planarity : 0.004 0.047 1450 Dihedral : 5.463 59.206 1140 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.67 % Allowed : 8.44 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.26), residues: 1020 helix: 2.10 (0.57), residues: 55 sheet: 0.38 (0.25), residues: 415 loop : -0.58 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.014 0.001 TYR E 54 PHE 0.009 0.001 PHE E 52 TRP 0.006 0.001 TRP B 162 HIS 0.005 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8440) covalent geometry : angle 0.63795 / 0.33 (11480) SS BOND : bond 0.00151 / 0.08 ( 5) SS BOND : angle 0.34365 / 0.23 ( 10) hydrogen bonds : bond 0.03429 / 2.16 ( 327) hydrogen bonds : angle 5.27371 / 3.52 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.83 seconds wall clock time: 56 minutes 23.58 seconds (3383.58 seconds total)