Starting phenix.real_space_refine on Sat Sep 12 11:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.map" model { file = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zg8_11196/09_2026/6zg8_11196.cif" } resolution = 3.49 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 4996 2.51 5 N 1257 2.21 5 O 1417 1.98 5 H 7965 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 15672 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1961 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1078 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1078 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.15 Number of scatterers: 15672 At special positions: 0 Unit cell: (67.072, 74.408, 187.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 1417 8.00 N 1257 7.00 C 4996 6.00 H 7965 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.47 Conformation dependent library (CDL) restraints added in 438.0 milliseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 77.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.643A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.607A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.769A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.745A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.698A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 199 through 272 removed outlier: 3.548A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 119 Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 10 through 25 Processing helix chain 'I' and resid 29 through 39 removed outlier: 4.258A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 removed outlier: 4.343A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 39 removed outlier: 3.997A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 73 removed outlier: 3.943A pdb=" N LEU K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 removed outlier: 3.788A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 39 removed outlier: 3.738A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 74 removed outlier: 3.748A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'M' and resid 18 through 39 removed outlier: 3.708A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 3.991A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 3.513A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 41 No H-bonds generated for 'chain 'N' and resid 39 through 41' Processing helix chain 'N' and resid 42 through 73 removed outlier: 4.340A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 3.831A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 73 removed outlier: 4.732A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 3.993A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 removed outlier: 3.914A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 74 removed outlier: 4.989A pdb=" N MET P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 removed outlier: 3.647A pdb=" N THR Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 39 removed outlier: 4.097A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN Q 39 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 71 removed outlier: 4.813A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 15 Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.195A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 74 removed outlier: 5.443A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.300A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU G 125 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 26 through 31 removed outlier: 5.030A pdb=" N PHE H 18 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 44 through 47 removed outlier: 6.933A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1920 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: 3.74 Time building geometry restraints manager: 1.87 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: 7811 1.03 - 1.23: 186 1.23 - 1.42: 3159 1.42 - 1.62: 4567 1.62 - 1.81: 64 Bond restraints: 15787 Sorted by residual: bond pdb=" CA M3L N 43 " pdb=" HA M3L N 43 " ideal model delta sigma weight residual 0.970 1.134 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" CA M3L P 43 " pdb=" HA M3L P 43 " ideal model delta sigma weight residual 0.970 1.134 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" CA M3L Q 43 " pdb=" HA M3L Q 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" CA M3L M 43 " pdb=" HA M3L M 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L O 43 " pdb=" HA M3L O 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.62e+01 ... (remaining 15782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 28081 1.71 - 3.41: 432 3.41 - 5.12: 45 5.12 - 6.82: 7 6.82 - 8.53: 2 Bond angle restraints: 28567 Sorted by residual: angle pdb=" N THR H 40 " pdb=" CA THR H 40 " pdb=" C THR H 40 " ideal model delta sigma weight residual 111.71 116.82 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" C GLY L 53 " pdb=" N PHE L 54 " pdb=" CA PHE L 54 " ideal model delta sigma weight residual 120.31 115.33 4.98 1.52e+00 4.33e-01 1.07e+01 angle pdb=" N ILE G 169 " pdb=" CA ILE G 169 " pdb=" C ILE G 169 " ideal model delta sigma weight residual 112.96 109.81 3.15 1.00e+00 1.00e+00 9.89e+00 angle pdb=" N PHE L 54 " pdb=" CA PHE L 54 " pdb=" CB PHE L 54 " ideal model delta sigma weight residual 110.28 114.74 -4.46 1.55e+00 4.16e-01 8.27e+00 angle pdb=" N GLU K 58 " pdb=" CA GLU K 58 " pdb=" CB GLU K 58 " ideal model delta sigma weight residual 110.22 114.51 -4.29 1.54e+00 4.22e-01 7.76e+00 ... (remaining 28562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6473 17.90 - 35.81: 557 35.81 - 53.71: 232 53.71 - 71.61: 72 71.61 - 89.51: 10 Dihedral angle restraints: 7344 sinusoidal: 3913 harmonic: 3431 Sorted by residual: dihedral pdb=" CA LEU R 56 " pdb=" C LEU R 56 " pdb=" N SER R 57 " pdb=" CA SER R 57 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE I 44 " pdb=" C ILE I 44 " pdb=" N VAL I 45 " pdb=" CA VAL I 45 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA H 21 " pdb=" C ALA H 21 " pdb=" N SER H 22 " pdb=" CA SER H 22 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 7341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 824 0.035 - 0.070: 313 0.070 - 0.105: 72 0.105 - 0.140: 38 0.140 - 0.175: 4 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CG LEU R 56 " pdb=" CB LEU R 56 " pdb=" CD1 LEU R 56 " pdb=" CD2 LEU R 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA MET K 60 " pdb=" N MET K 60 " pdb=" C MET K 60 " pdb=" CB MET K 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA M3L M 43 " pdb=" N M3L M 43 " pdb=" C M3L M 43 " pdb=" CB M3L M 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1248 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 52 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU L 52 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU L 52 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY L 53 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 54 " -0.013 2.00e-02 2.50e+03 1.04e-02 3.22e+00 pdb=" CG PHE K 54 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE K 54 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 54 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE K 54 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE K 54 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE K 54 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE K 54 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE K 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE K 54 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE K 54 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 54 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 66 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C MET L 66 " -0.030 2.00e-02 2.50e+03 pdb=" O MET L 66 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL L 67 " 0.010 2.00e-02 2.50e+03 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1674 2.23 - 2.82: 35594 2.82 - 3.41: 44457 3.41 - 4.01: 58870 4.01 - 4.60: 91524 Nonbonded interactions: 232119 Sorted by model distance: nonbonded pdb=" OD1 ASP G 74 " pdb=" H ASP G 110 " model vdw 1.637 2.450 nonbonded pdb=" OE1 GLN L 45 " pdb=" H GLN L 45 " model vdw 1.644 2.450 nonbonded pdb=" OD1 ASP Q 3 " pdb=" H THR Q 4 " model vdw 1.660 2.450 nonbonded pdb=" O SER G 180 " pdb=" H THR G 183 " model vdw 1.675 2.450 nonbonded pdb=" HG1 THR G 137 " pdb=" O GLY I 39 " model vdw 1.684 2.450 ... (remaining 232114 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 'K' selection = (chain 'L' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'M' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'N' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'O' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'P' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = chain 'Q' selection = (chain 'R' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.780 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.006 0.081 7822 Z= 0.268 Angle : 0.687 8.530 10565 Z= 0.383 Chirality : 0.042 0.175 1251 Planarity : 0.004 0.039 1321 Dihedral : 14.972 89.513 2712 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.37 (0.27), residues: 999 helix: 0.95 (0.19), residues: 736 sheet: -0.79 (0.61), residues: 77 loop : -1.94 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 252 TYR 0.016 0.002 TYR G 44 PHE 0.028 0.002 PHE K 54 TRP 0.004 0.001 TRP I 4 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 ( 7822) covalent geometry : angle 0.68702 / 0.38 (10565) hydrogen bonds : bond 0.10628 / 6.45 ( 648) hydrogen bonds : angle 5.01347 / 3.66 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 41 THR cc_start: 0.8295 (p) cc_final: 0.7961 (m) REVERT: Q 70 LEU cc_start: 0.8055 (mt) cc_final: 0.7835 (mt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1646 time to fit residues: 36.3544 Evaluate side-chains 132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105743 restraints weight = 30696.762| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.73 r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7822 Z= 0.142 Angle : 0.532 5.810 10565 Z= 0.288 Chirality : 0.038 0.140 1251 Planarity : 0.003 0.030 1321 Dihedral : 6.697 57.168 1127 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % 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: 1.29 (0.27), residues: 999 helix: 1.54 (0.19), residues: 757 sheet: -0.85 (0.56), residues: 89 loop : -1.37 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 252 TYR 0.011 0.001 TYR G 44 PHE 0.030 0.002 PHE L 54 TRP 0.004 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7822) covalent geometry : angle 0.53211 / 0.29 (10565) hydrogen bonds : bond 0.04254 / 2.90 ( 648) hydrogen bonds : angle 3.83470 / 2.77 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.6700 (mmp) cc_final: 0.6499 (mtt) REVERT: G 156 ASP cc_start: 0.8227 (m-30) cc_final: 0.7976 (m-30) REVERT: I 41 THR cc_start: 0.8390 (p) cc_final: 0.8021 (m) REVERT: K 15 THR cc_start: 0.8972 (t) cc_final: 0.8721 (m) REVERT: Q 70 LEU cc_start: 0.8115 (mt) cc_final: 0.7903 (mt) outliers start: 5 outliers final: 3 residues processed: 152 average time/residue: 0.1638 time to fit residues: 35.8170 Evaluate side-chains 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain Q residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN O 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105062 restraints weight = 30961.944| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.73 r_work: 0.3161 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7822 Z= 0.171 Angle : 0.527 6.565 10565 Z= 0.286 Chirality : 0.037 0.140 1251 Planarity : 0.003 0.031 1321 Dihedral : 6.616 58.185 1127 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.04 % Allowed : 9.53 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.27), residues: 999 helix: 1.87 (0.19), residues: 748 sheet: -0.86 (0.56), residues: 89 loop : -1.36 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 252 TYR 0.011 0.001 TYR G 171 PHE 0.013 0.002 PHE R 29 TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 7822) covalent geometry : angle 0.52654 / 0.29 (10565) hydrogen bonds : bond 0.04230 / 2.89 ( 648) hydrogen bonds : angle 3.71776 / 2.69 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: G 156 ASP cc_start: 0.8158 (m-30) cc_final: 0.7886 (m-30) REVERT: I 41 THR cc_start: 0.8366 (p) cc_final: 0.8007 (m) REVERT: K 15 THR cc_start: 0.9012 (t) cc_final: 0.8773 (m) REVERT: Q 54 PHE cc_start: 0.7892 (t80) cc_final: 0.7680 (t80) REVERT: Q 70 LEU cc_start: 0.8118 (mt) cc_final: 0.7905 (mt) outliers start: 8 outliers final: 6 residues processed: 146 average time/residue: 0.1705 time to fit residues: 35.6389 Evaluate side-chains 144 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain Q residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104749 restraints weight = 30747.600| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7822 Z= 0.177 Angle : 0.527 5.657 10565 Z= 0.286 Chirality : 0.038 0.139 1251 Planarity : 0.003 0.032 1321 Dihedral : 6.620 59.787 1127 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.17 % Allowed : 11.62 % Favored : 87.21 % 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: 1.74 (0.27), residues: 999 helix: 1.95 (0.19), residues: 750 sheet: -0.86 (0.56), residues: 89 loop : -1.42 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 252 TYR 0.016 0.001 TYR G 171 PHE 0.018 0.002 PHE P 54 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 7822) covalent geometry : angle 0.52698 / 0.29 (10565) hydrogen bonds : bond 0.04171 / 2.85 ( 648) hydrogen bonds : angle 3.63732 / 2.64 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: G 156 ASP cc_start: 0.8154 (m-30) cc_final: 0.7875 (m-30) REVERT: I 41 THR cc_start: 0.8360 (p) cc_final: 0.7993 (m) REVERT: K 15 THR cc_start: 0.9034 (t) cc_final: 0.8789 (m) REVERT: P 54 PHE cc_start: 0.8249 (t80) cc_final: 0.8027 (t80) REVERT: Q 54 PHE cc_start: 0.7953 (t80) cc_final: 0.7748 (t80) REVERT: Q 70 LEU cc_start: 0.8106 (mt) cc_final: 0.7895 (mt) outliers start: 9 outliers final: 9 residues processed: 148 average time/residue: 0.1542 time to fit residues: 33.2485 Evaluate side-chains 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 255 GLN N 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105126 restraints weight = 30625.648| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.72 r_work: 0.3165 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7822 Z= 0.168 Angle : 0.519 5.276 10565 Z= 0.280 Chirality : 0.037 0.139 1251 Planarity : 0.003 0.031 1321 Dihedral : 6.582 59.162 1127 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.70 % Allowed : 12.27 % Favored : 86.03 % 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: 1.89 (0.27), residues: 999 helix: 2.06 (0.18), residues: 750 sheet: -0.86 (0.56), residues: 89 loop : -1.38 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 252 TYR 0.011 0.001 TYR I 11 PHE 0.016 0.002 PHE P 54 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 7822) covalent geometry : angle 0.51881 / 0.28 (10565) hydrogen bonds : bond 0.04071 / 2.79 ( 648) hydrogen bonds : angle 3.57758 / 2.60 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: G 156 ASP cc_start: 0.8140 (m-30) cc_final: 0.7870 (m-30) REVERT: I 41 THR cc_start: 0.8350 (p) cc_final: 0.7985 (m) REVERT: K 15 THR cc_start: 0.9053 (t) cc_final: 0.8822 (m) REVERT: K 60 MET cc_start: 0.7532 (mmm) cc_final: 0.7251 (mmp) REVERT: L 49 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7863 (m-10) REVERT: Q 54 PHE cc_start: 0.8024 (t80) cc_final: 0.7795 (t80) REVERT: Q 70 LEU cc_start: 0.8106 (mt) cc_final: 0.7893 (mt) outliers start: 13 outliers final: 9 residues processed: 150 average time/residue: 0.1527 time to fit residues: 33.8557 Evaluate side-chains 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104742 restraints weight = 30648.604| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.72 r_work: 0.3155 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7822 Z= 0.177 Angle : 0.526 5.713 10565 Z= 0.284 Chirality : 0.037 0.139 1251 Planarity : 0.003 0.033 1321 Dihedral : 6.586 58.391 1127 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.44 % Allowed : 13.71 % Favored : 84.86 % 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: 1.94 (0.27), residues: 999 helix: 2.10 (0.18), residues: 750 sheet: -0.85 (0.56), residues: 89 loop : -1.40 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 252 TYR 0.012 0.001 TYR G 171 PHE 0.015 0.002 PHE Q 29 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 7822) covalent geometry : angle 0.52574 / 0.28 (10565) hydrogen bonds : bond 0.04126 / 2.82 ( 648) hydrogen bonds : angle 3.55634 / 2.59 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: G 110 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6807 (t70) REVERT: G 156 ASP cc_start: 0.8150 (m-30) cc_final: 0.7881 (m-30) REVERT: I 41 THR cc_start: 0.8343 (p) cc_final: 0.7975 (m) REVERT: K 15 THR cc_start: 0.9072 (t) cc_final: 0.8848 (m) REVERT: K 60 MET cc_start: 0.7321 (mmm) cc_final: 0.7112 (mmp) REVERT: L 49 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7903 (m-10) REVERT: Q 54 PHE cc_start: 0.7983 (t80) cc_final: 0.7763 (t80) REVERT: Q 70 LEU cc_start: 0.8112 (mt) cc_final: 0.7899 (mt) outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.1642 time to fit residues: 34.5610 Evaluate side-chains 147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105309 restraints weight = 30652.573| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.72 r_work: 0.3170 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.159 Angle : 0.514 6.393 10565 Z= 0.277 Chirality : 0.037 0.144 1251 Planarity : 0.003 0.040 1321 Dihedral : 6.552 57.800 1127 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.57 % Allowed : 13.58 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.27), residues: 999 helix: 2.18 (0.18), residues: 750 sheet: -0.84 (0.56), residues: 89 loop : -1.34 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 252 TYR 0.011 0.001 TYR G 44 PHE 0.014 0.001 PHE H 45 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7822) covalent geometry : angle 0.51445 / 0.28 (10565) hydrogen bonds : bond 0.03988 / 2.72 ( 648) hydrogen bonds : angle 3.49728 / 2.55 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: G 110 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6803 (t70) REVERT: G 156 ASP cc_start: 0.8109 (m-30) cc_final: 0.7840 (m-30) REVERT: I 41 THR cc_start: 0.8335 (p) cc_final: 0.7972 (m) REVERT: K 15 THR cc_start: 0.9061 (t) cc_final: 0.8831 (m) REVERT: K 60 MET cc_start: 0.7283 (mmm) cc_final: 0.6987 (mmp) REVERT: L 49 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7911 (m-10) REVERT: Q 54 PHE cc_start: 0.7976 (t80) cc_final: 0.7761 (t80) REVERT: Q 70 LEU cc_start: 0.8117 (mt) cc_final: 0.7900 (mt) outliers start: 12 outliers final: 7 residues processed: 150 average time/residue: 0.1616 time to fit residues: 35.4298 Evaluate side-chains 144 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 0.0370 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105285 restraints weight = 30757.942| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.73 r_work: 0.3174 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7822 Z= 0.148 Angle : 0.508 5.869 10565 Z= 0.272 Chirality : 0.037 0.177 1251 Planarity : 0.003 0.046 1321 Dihedral : 6.506 57.330 1127 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.17 % Allowed : 15.01 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.27), residues: 999 helix: 2.26 (0.19), residues: 750 sheet: -0.82 (0.55), residues: 89 loop : -1.28 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 252 TYR 0.011 0.001 TYR G 44 PHE 0.015 0.001 PHE K 54 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7822) covalent geometry : angle 0.50767 / 0.27 (10565) hydrogen bonds : bond 0.03880 / 2.65 ( 648) hydrogen bonds : angle 3.44904 / 2.51 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: G 156 ASP cc_start: 0.8141 (m-30) cc_final: 0.7884 (m-30) REVERT: I 41 THR cc_start: 0.8328 (p) cc_final: 0.7955 (m) REVERT: K 15 THR cc_start: 0.9062 (t) cc_final: 0.8820 (m) REVERT: K 60 MET cc_start: 0.7314 (mmm) cc_final: 0.7106 (mmp) REVERT: L 49 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: Q 54 PHE cc_start: 0.7983 (t80) cc_final: 0.7783 (t80) REVERT: Q 70 LEU cc_start: 0.8111 (mt) cc_final: 0.7894 (mt) outliers start: 9 outliers final: 7 residues processed: 143 average time/residue: 0.1544 time to fit residues: 32.9810 Evaluate side-chains 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104595 restraints weight = 30753.916| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.73 r_work: 0.3158 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.177 Angle : 0.530 5.594 10565 Z= 0.285 Chirality : 0.038 0.185 1251 Planarity : 0.003 0.037 1321 Dihedral : 6.543 56.811 1127 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.44 % Allowed : 15.27 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.27), residues: 999 helix: 2.20 (0.19), residues: 750 sheet: -0.82 (0.55), residues: 89 loop : -1.36 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 252 TYR 0.012 0.001 TYR G 44 PHE 0.015 0.002 PHE K 54 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 7822) covalent geometry : angle 0.52987 / 0.29 (10565) hydrogen bonds : bond 0.04064 / 2.77 ( 648) hydrogen bonds : angle 3.49640 / 2.54 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: G 110 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6806 (t70) REVERT: G 156 ASP cc_start: 0.8121 (m-30) cc_final: 0.7849 (m-30) REVERT: I 41 THR cc_start: 0.8327 (p) cc_final: 0.7956 (m) REVERT: K 2 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6165 (tt) REVERT: K 15 THR cc_start: 0.9070 (t) cc_final: 0.8840 (m) REVERT: L 49 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: L 51 ILE cc_start: 0.7959 (mm) cc_final: 0.7745 (mt) REVERT: Q 70 LEU cc_start: 0.8117 (mt) cc_final: 0.7898 (mt) outliers start: 11 outliers final: 7 residues processed: 145 average time/residue: 0.1502 time to fit residues: 32.1235 Evaluate side-chains 148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 83 optimal weight: 0.0270 chunk 51 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107129 restraints weight = 30336.439| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.71 r_work: 0.3199 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7822 Z= 0.122 Angle : 0.496 6.328 10565 Z= 0.263 Chirality : 0.037 0.170 1251 Planarity : 0.003 0.039 1321 Dihedral : 6.439 56.471 1127 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.17 % Allowed : 15.40 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.27), residues: 999 helix: 2.45 (0.19), residues: 750 sheet: -0.82 (0.55), residues: 89 loop : -1.15 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 252 TYR 0.013 0.001 TYR G 44 PHE 0.018 0.001 PHE K 54 TRP 0.003 0.001 TRP I 4 HIS 0.001 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7822) covalent geometry : angle 0.49645 / 0.26 (10565) hydrogen bonds : bond 0.03645 / 2.49 ( 648) hydrogen bonds : angle 3.37351 / 2.46 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: G 110 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6889 (t70) REVERT: G 156 ASP cc_start: 0.8130 (m-30) cc_final: 0.7878 (m-30) REVERT: I 41 THR cc_start: 0.8289 (p) cc_final: 0.7850 (m) REVERT: K 15 THR cc_start: 0.9026 (t) cc_final: 0.8768 (m) REVERT: L 49 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: Q 66 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6198 (ptp) REVERT: Q 70 LEU cc_start: 0.8093 (mt) cc_final: 0.7855 (mt) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 0.1366 time to fit residues: 30.7904 Evaluate side-chains 152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 ASN P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105959 restraints weight = 30561.940| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.75 r_work: 0.3183 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7822 Z= 0.147 Angle : 0.517 6.967 10565 Z= 0.273 Chirality : 0.037 0.163 1251 Planarity : 0.003 0.034 1321 Dihedral : 6.454 56.184 1127 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.17 % Allowed : 15.80 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.27), residues: 999 helix: 2.44 (0.19), residues: 748 sheet: -0.81 (0.55), residues: 89 loop : -1.19 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 252 TYR 0.012 0.001 TYR G 44 PHE 0.020 0.001 PHE O 54 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7822) covalent geometry : angle 0.51655 / 0.27 (10565) hydrogen bonds : bond 0.03783 / 2.57 ( 648) hydrogen bonds : angle 3.38995 / 2.47 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.04 seconds wall clock time: 65 minutes 5.27 seconds (3905.27 seconds total)