Starting phenix.real_space_refine on Sat Sep 12 13:45:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pke_13469/09_2026/7pke_13469_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pke_13469/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pke_13469/09_2026/7pke_13469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pke_13469/09_2026/7pke_13469.map" model { file = "/net/cci-nas-00/data/ceres_data/7pke_13469/09_2026/7pke_13469_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pke_13469/09_2026/7pke_13469_trim.cif" } 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-2.2.1-6174/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, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 3.17, per 1000 atoms: 0.20 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: 1.51 Conformation dependent library (CDL) restraints added in 634.9 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: 0.49 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: 3.76 Time building geometry restraints manager: 2.03 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: 0.01 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: 4.620 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: 0.110 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- 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 : 0.320 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: 0.2846 time to fit residues: 39.1926 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 : 0.468 ------------------------------------------------------------------------------- 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: 0.1980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.2660 r_free = 0.2660 target = 0.074395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.061176 restraints weight = 37779.656| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.08 r_work: 0.2339 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2200 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1439 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= 0.129 Angle : 0.705 15.310 11490 Z= 0.375 Chirality : 0.133 1.676 1235 Planarity : 0.004 0.062 1450 Dihedral : 7.011 58.276 1140 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 1.72 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: 2.26 (0.69), residues: 55 sheet: 0.38 (0.24), residues: 415 loop : -0.28 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 188 TYR 0.024 0.001 TYR E 54 PHE 0.016 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 0.00294 / 0.13 ( 8440) covalent geometry : angle 0.70554 / 0.38 (11480) SS BOND : bond 0.00177 / 0.10 ( 5) SS BOND : angle 0.53640 / 0.32 ( 10) hydrogen bonds : bond 0.04627 / 2.99 ( 327) hydrogen bonds : angle 5.93670 / 3.96 ( 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 119 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8509 (p0) cc_final: 0.7912 (p0) REVERT: D 188 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8493 (mtm-85) REVERT: C 28 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7918 (ttpt) REVERT: B 16 ASP cc_start: 0.8541 (p0) cc_final: 0.8042 (p0) REVERT: B 59 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8439 (tp-100) REVERT: A 16 ASP cc_start: 0.8433 (p0) cc_final: 0.8049 (p0) REVERT: A 188 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8410 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 119 average time/residue: 0.2818 time to fit residues: 42.9774 Evaluate side-chains 93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.2639 r_free = 0.2639 target = 0.073265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.060370 restraints weight = 38751.434| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 2.09 r_work: 0.2314 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1845 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= 0.160 Angle : 0.676 15.686 11490 Z= 0.359 Chirality : 0.133 1.687 1235 Planarity : 0.004 0.041 1450 Dihedral : 6.781 56.574 1140 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.44 % Allowed : 4.22 % 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: 0.05 (0.25), residues: 1020 helix: 2.33 (0.63), residues: 55 sheet: 0.32 (0.22), residues: 445 loop : -0.41 (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 0.011 0.001 PHE B 66 TRP 0.008 0.001 TRP A 162 HIS 0.010 0.005 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8440) covalent geometry : angle 0.67588 / 0.36 (11480) SS BOND : bond 0.00092 / 0.05 ( 5) SS BOND : angle 0.63800 / 0.40 ( 10) hydrogen bonds : bond 0.04372 / 2.79 ( 327) hydrogen bonds : angle 5.64101 / 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 98 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 ASP cc_start: 0.8650 (p0) cc_final: 0.8360 (p0) REVERT: D 188 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8449 (mtm-85) REVERT: C 28 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7953 (ttpt) REVERT: B 16 ASP cc_start: 0.8568 (p0) cc_final: 0.8042 (p0) REVERT: B 59 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8455 (tp-100) REVERT: B 163 ASP cc_start: 0.8675 (p0) cc_final: 0.8237 (p0) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.2843 time to fit residues: 35.0850 Evaluate side-chains 94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.2598 r_free = 0.2598 target = 0.071079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.058096 restraints weight = 38624.719| |-----------------------------------------------------------------------------| r_work (start): 0.2371 rms_B_bonded: 2.08 r_work: 0.2263 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2126 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8445 Z= 0.237 Angle : 0.685 15.838 11490 Z= 0.364 Chirality : 0.134 1.688 1235 Planarity : 0.004 0.032 1450 Dihedral : 6.107 49.476 1140 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.56 % Allowed : 6.33 % Favored : 93.11 % 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: -0.11 (0.25), residues: 1020 helix: 2.19 (0.61), residues: 55 sheet: 0.22 (0.23), residues: 445 loop : -0.52 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 188 TYR 0.023 0.002 TYR E 54 PHE 0.012 0.001 PHE B 66 TRP 0.010 0.001 TRP E 162 HIS 0.011 0.003 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 8440) covalent geometry : angle 0.68554 / 0.36 (11480) SS BOND : bond 0.00135 / 0.07 ( 5) SS BOND : angle 0.36618 / 0.24 ( 10) hydrogen bonds : bond 0.04305 / 2.76 ( 327) hydrogen bonds : angle 5.49982 / 3.67 ( 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 106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.460 Fit side-chains REVERT: E 28 LYS cc_start: 0.8220 (ttpt) cc_final: 0.8017 (ttpt) REVERT: D 16 ASP cc_start: 0.8619 (p0) cc_final: 0.8234 (p0) REVERT: B 16 ASP cc_start: 0.8610 (p0) cc_final: 0.8102 (p0) REVERT: B 125 TYR cc_start: 0.8898 (t80) cc_final: 0.8659 (t80) outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.3036 time to fit residues: 39.9689 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR 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: 0.9980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.072966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.059666 restraints weight = 38253.619| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 2.11 r_work: 0.2286 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2150 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2367 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= 0.161 Angle : 0.653 15.750 11490 Z= 0.343 Chirality : 0.133 1.689 1235 Planarity : 0.004 0.057 1450 Dihedral : 5.764 42.952 1140 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.44 % Allowed : 7.44 % Favored : 92.11 % 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: -0.03 (0.25), residues: 1020 helix: 2.01 (0.57), residues: 55 sheet: 0.36 (0.24), residues: 415 loop : -0.48 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 188 TYR 0.018 0.001 TYR E 54 PHE 0.010 0.001 PHE A 52 TRP 0.007 0.001 TRP B 110 HIS 0.007 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 8440) covalent geometry : angle 0.65305 / 0.34 (11480) SS BOND : bond 0.00135 / 0.08 ( 5) SS BOND : angle 0.39713 / 0.27 ( 10) hydrogen bonds : bond 0.03740 / 2.39 ( 327) hydrogen bonds : angle 5.41298 / 3.61 ( 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 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.463 Fit side-chains REVERT: D 16 ASP cc_start: 0.8576 (p0) cc_final: 0.8187 (p0) REVERT: D 163 ASP cc_start: 0.8644 (p0) cc_final: 0.8417 (p0) REVERT: C 188 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8239 (mtt90) REVERT: B 16 ASP cc_start: 0.8560 (p0) cc_final: 0.8070 (p0) REVERT: B 125 TYR cc_start: 0.8842 (t80) cc_final: 0.8568 (t80) REVERT: B 163 ASP cc_start: 0.8699 (p0) cc_final: 0.8329 (p0) outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.2859 time to fit residues: 35.6593 Evaluate side-chains 93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.072833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.059526 restraints weight = 38191.737| |-----------------------------------------------------------------------------| r_work (start): 0.2391 rms_B_bonded: 2.12 r_work: 0.2285 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2150 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2503 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= 0.159 Angle : 0.645 15.751 11490 Z= 0.338 Chirality : 0.133 1.689 1235 Planarity : 0.004 0.052 1450 Dihedral : 5.649 46.715 1140 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.67 % Allowed : 7.78 % 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: -0.04 (0.26), residues: 1020 helix: 1.94 (0.58), residues: 55 sheet: 0.33 (0.24), residues: 415 loop : -0.47 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 188 TYR 0.016 0.001 TYR E 54 PHE 0.010 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 0.00379 / 0.16 ( 8440) covalent geometry : angle 0.64521 / 0.34 (11480) SS BOND : bond 0.00147 / 0.08 ( 5) SS BOND : angle 0.34605 / 0.23 ( 10) hydrogen bonds : bond 0.03646 / 2.32 ( 327) hydrogen bonds : angle 5.34341 / 3.56 ( 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 105 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.482 Fit side-chains REVERT: D 13 LYS cc_start: 0.8733 (mttt) cc_final: 0.8481 (mmtt) REVERT: D 16 ASP cc_start: 0.8574 (p0) cc_final: 0.8173 (p0) REVERT: D 163 ASP cc_start: 0.8620 (p0) cc_final: 0.8399 (p0) REVERT: C 188 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8238 (mtt90) REVERT: B 125 TYR cc_start: 0.8859 (t80) cc_final: 0.8579 (t80) REVERT: B 163 ASP cc_start: 0.8679 (p0) cc_final: 0.8301 (p0) REVERT: A 163 ASP cc_start: 0.8514 (p0) cc_final: 0.8253 (p0) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2898 time to fit residues: 39.0714 Evaluate side-chains 93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR 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: 1.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.072934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.059584 restraints weight = 38233.966| |-----------------------------------------------------------------------------| r_work (start): 0.2379 rms_B_bonded: 2.13 r_work: 0.2272 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8445 Z= 0.173 Angle : 0.650 15.775 11490 Z= 0.342 Chirality : 0.133 1.693 1235 Planarity : 0.004 0.058 1450 Dihedral : 5.718 51.075 1140 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.78 % Allowed : 7.78 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1020 helix: 1.94 (0.57), residues: 55 sheet: 0.32 (0.24), residues: 415 loop : -0.53 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 188 TYR 0.016 0.001 TYR E 54 PHE 0.010 0.001 PHE E 52 TRP 0.006 0.001 TRP B 162 HIS 0.006 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8440) covalent geometry : angle 0.65058 / 0.34 (11480) SS BOND : bond 0.00128 / 0.07 ( 5) SS BOND : angle 0.34236 / 0.23 ( 10) hydrogen bonds : bond 0.03673 / 2.34 ( 327) hydrogen bonds : angle 5.33670 / 3.56 ( 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 106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.587 Fit side-chains REVERT: E 1 GLN cc_start: 0.8281 (mp10) cc_final: 0.7936 (mm-40) REVERT: D 13 LYS cc_start: 0.8767 (mttt) cc_final: 0.8515 (mmtt) REVERT: D 16 ASP cc_start: 0.8616 (p0) cc_final: 0.8217 (p0) REVERT: D 163 ASP cc_start: 0.8629 (p0) cc_final: 0.8412 (p0) REVERT: C 188 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8293 (mtt90) REVERT: B 125 TYR cc_start: 0.8913 (t80) cc_final: 0.8623 (t80) REVERT: B 163 ASP cc_start: 0.8652 (p0) cc_final: 0.8259 (p0) REVERT: A 163 ASP cc_start: 0.8496 (p0) cc_final: 0.8237 (p0) outliers start: 7 outliers final: 3 residues processed: 106 average time/residue: 0.2940 time to fit residues: 39.8639 Evaluate side-chains 98 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR 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: 0.5980 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2638 r_free = 0.2638 target = 0.073372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.059862 restraints weight = 38126.593| |-----------------------------------------------------------------------------| r_work (start): 0.2377 rms_B_bonded: 2.16 r_work: 0.2271 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2135 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2725 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= 0.157 Angle : 0.643 15.745 11490 Z= 0.337 Chirality : 0.133 1.695 1235 Planarity : 0.004 0.059 1450 Dihedral : 5.739 56.527 1140 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.78 % Allowed : 8.00 % 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: -0.10 (0.26), residues: 1020 helix: 1.94 (0.57), residues: 55 sheet: 0.33 (0.24), residues: 415 loop : -0.55 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 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 B 162 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8440) covalent geometry : angle 0.64327 / 0.34 (11480) SS BOND : bond 0.00150 / 0.08 ( 5) SS BOND : angle 0.31216 / 0.21 ( 10) hydrogen bonds : bond 0.03567 / 2.27 ( 327) hydrogen bonds : angle 5.31307 / 3.54 ( 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 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.376 Fit side-chains REVERT: E 1 GLN cc_start: 0.8272 (mp10) cc_final: 0.7919 (mm110) REVERT: D 13 LYS cc_start: 0.8764 (mttt) cc_final: 0.8511 (mmtt) REVERT: D 16 ASP cc_start: 0.8602 (p0) cc_final: 0.8206 (p0) REVERT: D 163 ASP cc_start: 0.8605 (p0) cc_final: 0.8389 (p0) REVERT: C 188 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8329 (mtt90) REVERT: B 125 TYR cc_start: 0.8910 (t80) cc_final: 0.8609 (t80) REVERT: B 163 ASP cc_start: 0.8641 (p0) cc_final: 0.8237 (p0) REVERT: A 163 ASP cc_start: 0.8504 (p0) cc_final: 0.8250 (p0) outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 0.2810 time to fit residues: 39.2414 Evaluate side-chains 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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** A 1 GLN A 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.073648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.060240 restraints weight = 37880.644| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 2.14 r_work: 0.2281 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2146 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2788 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= 0.161 Angle : 0.643 15.747 11490 Z= 0.337 Chirality : 0.133 1.699 1235 Planarity : 0.004 0.052 1450 Dihedral : 5.707 57.631 1140 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.67 % Allowed : 8.22 % Favored : 91.11 % 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: -0.11 (0.26), residues: 1020 helix: 1.93 (0.57), residues: 55 sheet: 0.33 (0.25), residues: 415 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 188 TYR 0.015 0.001 TYR E 54 PHE 0.013 0.001 PHE B 180 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 0.00386 / 0.16 ( 8440) covalent geometry : angle 0.64293 / 0.34 (11480) SS BOND : bond 0.00153 / 0.09 ( 5) SS BOND : angle 0.31862 / 0.21 ( 10) hydrogen bonds : bond 0.03568 / 2.26 ( 327) hydrogen bonds : angle 5.29813 / 3.54 ( 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 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8752 (mttt) cc_final: 0.8497 (mmtt) REVERT: D 16 ASP cc_start: 0.8593 (p0) cc_final: 0.8207 (p0) REVERT: D 163 ASP cc_start: 0.8592 (p0) cc_final: 0.8376 (p0) REVERT: C 188 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8341 (mtt90) REVERT: B 125 TYR cc_start: 0.8912 (t80) cc_final: 0.8607 (t80) REVERT: B 163 ASP cc_start: 0.8626 (p0) cc_final: 0.8231 (p0) outliers start: 6 outliers final: 5 residues processed: 107 average time/residue: 0.2920 time to fit residues: 40.0604 Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 HIS 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: 0.9980 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.2640 r_free = 0.2640 target = 0.073522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.060148 restraints weight = 37772.848| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 2.13 r_work: 0.2318 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2181 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2835 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= 0.151 Angle : 0.643 15.747 11490 Z= 0.337 Chirality : 0.133 1.701 1235 Planarity : 0.004 0.066 1450 Dihedral : 5.452 49.503 1140 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.56 % Allowed : 8.67 % Favored : 90.78 % 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 (0.26), residues: 1020 helix: 1.94 (0.57), residues: 55 sheet: 0.33 (0.25), residues: 415 loop : -0.55 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 188 TYR 0.014 0.001 TYR E 54 PHE 0.010 0.001 PHE B 180 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 0.00365 / 0.15 ( 8440) covalent geometry : angle 0.64308 / 0.34 (11480) SS BOND : bond 0.00158 / 0.09 ( 5) SS BOND : angle 0.33411 / 0.23 ( 10) hydrogen bonds : bond 0.03480 / 2.20 ( 327) hydrogen bonds : angle 5.28604 / 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 106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8740 (mttt) cc_final: 0.8509 (mmtt) REVERT: D 16 ASP cc_start: 0.8598 (p0) cc_final: 0.8209 (p0) REVERT: D 163 ASP cc_start: 0.8595 (p0) cc_final: 0.8384 (p0) REVERT: C 188 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8351 (mtt90) REVERT: B 125 TYR cc_start: 0.8923 (t80) cc_final: 0.8619 (t80) REVERT: A 163 ASP cc_start: 0.8524 (p0) cc_final: 0.8308 (p0) outliers start: 5 outliers final: 5 residues processed: 106 average time/residue: 0.2989 time to fit residues: 40.3700 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 HIS 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: 0.6980 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.2647 r_free = 0.2647 target = 0.073904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.060678 restraints weight = 37723.591| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 2.11 r_work: 0.2394 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2256 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2904 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= 0.129 Angle : 0.635 15.694 11490 Z= 0.332 Chirality : 0.133 1.700 1235 Planarity : 0.004 0.059 1450 Dihedral : 5.197 43.524 1140 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.67 % Allowed : 8.67 % Favored : 90.67 % 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: -0.07 (0.26), residues: 1020 helix: 1.98 (0.57), residues: 55 sheet: 0.34 (0.25), residues: 415 loop : -0.52 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 188 TYR 0.013 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 0.00314 / 0.13 ( 8440) covalent geometry : angle 0.63494 / 0.33 (11480) SS BOND : bond 0.00162 / 0.09 ( 5) SS BOND : angle 0.35937 / 0.25 ( 10) hydrogen bonds : bond 0.03331 / 2.10 ( 327) hydrogen bonds : angle 5.25553 / 3.51 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.98 seconds wall clock time: 64 minutes 38.07 seconds (3878.07 seconds total)