Starting phenix.real_space_refine on Mon Nov 17 16:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oh0_3809/11_2025/5oh0_3809.map" } resolution = 4.2 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 4032 2.51 5 N 1158 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.08, per 1000 atoms: 0.16 Number of scatterers: 6588 At special positions: 0 Unit cell: (87.01, 84.75, 84.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1386 8.00 N 1158 7.00 C 4032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " 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: 0.51 Conformation dependent library (CDL) restraints added in 398.3 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 5.2% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'F' and resid 25 through 28 removed outlier: 4.033A pdb=" N VAL F 28 " --> pdb=" O ALA F 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 28' Processing helix chain 'F' and resid 38 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR A 48 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA A 139 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 50 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A 137 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.967A pdb=" N GLN A 30 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS B 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 32 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU B 15 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE A 154 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR B 9 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 152 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.967A pdb=" N GLN A 30 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS B 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 32 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU B 15 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 148 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 16 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR B 48 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 139 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 50 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 137 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.970A pdb=" N GLN B 30 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LYS C 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 32 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLU C 15 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE B 154 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR C 9 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA B 152 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.970A pdb=" N GLN B 30 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LYS C 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 32 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLU C 15 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 148 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 16 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR C 48 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA C 139 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER C 50 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR C 137 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 35 removed outlier: 3.788A pdb=" N GLN C 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 32 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU D 15 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE C 154 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR D 9 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA C 152 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 35 removed outlier: 3.788A pdb=" N GLN C 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 32 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU D 15 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 148 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 16 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 23 removed outlier: 6.518A pdb=" N THR D 48 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA D 139 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER D 50 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR D 137 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.940A pdb=" N GLN D 30 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS E 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 32 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU E 15 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE D 154 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR E 9 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA D 152 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.940A pdb=" N GLN D 30 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS E 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 32 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU E 15 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 148 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 16 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 22 through 23 removed outlier: 6.518A pdb=" N THR E 48 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA E 139 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER E 50 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR E 137 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35 removed outlier: 3.720A pdb=" N GLN E 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 32 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU F 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE E 154 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR F 9 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA E 152 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 35 removed outlier: 3.720A pdb=" N GLN E 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 32 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU F 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 148 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 16 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR F 48 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA F 139 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 50 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR F 137 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 70 through 74 145 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2328 1.34 - 1.46: 1473 1.46 - 1.58: 2847 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 6660 Sorted by residual: bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.24e+00 bond pdb=" N GLY F 53 " pdb=" CA GLY F 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.18e+00 bond pdb=" N GLY E 53 " pdb=" CA GLY E 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.14e+00 bond pdb=" N GLY B 53 " pdb=" CA GLY B 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.11e+00 ... (remaining 6655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 8012 1.06 - 2.12: 877 2.12 - 3.19: 170 3.19 - 4.25: 32 4.25 - 5.31: 11 Bond angle restraints: 9102 Sorted by residual: angle pdb=" N ASP A 114 " pdb=" CA ASP A 114 " pdb=" C ASP A 114 " ideal model delta sigma weight residual 114.56 110.82 3.74 1.27e+00 6.20e-01 8.70e+00 angle pdb=" N ASP D 114 " pdb=" CA ASP D 114 " pdb=" C ASP D 114 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.59e+00 angle pdb=" N ASP C 114 " pdb=" CA ASP C 114 " pdb=" C ASP C 114 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.58e+00 angle pdb=" N ASP F 114 " pdb=" CA ASP F 114 " pdb=" C ASP F 114 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.48e+00 angle pdb=" N ASP B 114 " pdb=" CA ASP B 114 " pdb=" C ASP B 114 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.47e+00 ... (remaining 9097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 3710 14.28 - 28.57: 136 28.57 - 42.85: 30 42.85 - 57.13: 0 57.13 - 71.42: 6 Dihedral angle restraints: 3882 sinusoidal: 1242 harmonic: 2640 Sorted by residual: dihedral pdb=" CA PHE E 154 " pdb=" C PHE E 154 " pdb=" N LYS E 155 " pdb=" CA LYS E 155 " ideal model delta harmonic sigma weight residual 180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE D 154 " pdb=" C PHE D 154 " pdb=" N LYS D 155 " pdb=" CA LYS D 155 " ideal model delta harmonic sigma weight residual -180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE C 154 " pdb=" C PHE C 154 " pdb=" N LYS C 155 " pdb=" CA LYS C 155 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 614 0.030 - 0.059: 322 0.059 - 0.089: 113 0.089 - 0.119: 60 0.119 - 0.148: 31 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA VAL C 5 " pdb=" N VAL C 5 " pdb=" C VAL C 5 " pdb=" CB VAL C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL F 5 " pdb=" N VAL F 5 " pdb=" C VAL F 5 " pdb=" CB VAL F 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1137 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 131 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 131 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 132 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 131 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO C 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.022 5.00e-02 4.00e+02 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2071 2.82 - 3.34: 4982 3.34 - 3.86: 10156 3.86 - 4.38: 10347 4.38 - 4.90: 19483 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" OD1 ASN A 98 " pdb=" OG1 THR A 140 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASN D 98 " pdb=" OG1 THR D 140 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN E 98 " pdb=" OG1 THR E 140 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG1 THR B 140 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN C 98 " pdb=" OG1 THR C 140 " model vdw 2.296 3.040 ... (remaining 47034 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.460 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.003 0.023 6666 Z= 0.177 Angle : 0.751 5.312 9114 Z= 0.463 Chirality : 0.047 0.148 1140 Planarity : 0.004 0.039 1218 Dihedral : 8.942 71.416 2172 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.24), residues: 930 helix: None (None), residues: 0 sheet: -1.38 (0.38), residues: 216 loop : -3.13 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 106 TYR 0.002 0.001 TYR F 158 PHE 0.020 0.002 PHE E 154 HIS 0.001 0.000 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6660) covalent geometry : angle 0.75011 ( 9102) SS BOND : bond 0.00191 ( 6) SS BOND : angle 1.41601 ( 12) hydrogen bonds : bond 0.29446 ( 139) hydrogen bonds : angle 9.52740 ( 312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.259 Fit side-chains REVERT: F 29 ASP cc_start: 0.8339 (t70) cc_final: 0.8054 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0921 time to fit residues: 9.9366 Evaluate side-chains 23 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.041655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.036029 restraints weight = 40088.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.037111 restraints weight = 23222.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.037874 restraints weight = 15530.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.038398 restraints weight = 11404.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.038667 restraints weight = 8962.843| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6666 Z= 0.293 Angle : 0.660 9.623 9114 Z= 0.351 Chirality : 0.040 0.122 1140 Planarity : 0.003 0.032 1218 Dihedral : 5.106 16.122 966 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.90 % Allowed : 5.71 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.25), residues: 930 helix: None (None), residues: 0 sheet: -0.81 (0.37), residues: 216 loop : -2.81 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.009 0.001 TYR E 158 PHE 0.016 0.002 PHE A 73 HIS 0.003 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 6660) covalent geometry : angle 0.65844 ( 9102) SS BOND : bond 0.00102 ( 6) SS BOND : angle 1.49861 ( 12) hydrogen bonds : bond 0.03983 ( 139) hydrogen bonds : angle 6.33100 ( 312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.254 Fit side-chains REVERT: B 15 GLU cc_start: 0.8563 (tp30) cc_final: 0.8277 (tp30) REVERT: F 24 ASP cc_start: 0.8613 (t0) cc_final: 0.8401 (t0) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.0532 time to fit residues: 3.1768 Evaluate side-chains 19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.0060 chunk 1 optimal weight: 0.0020 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2738 r_free = 0.2738 target = 0.043493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.037699 restraints weight = 38173.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.038852 restraints weight = 21929.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.039683 restraints weight = 14461.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.040162 restraints weight = 10480.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.040638 restraints weight = 8362.859| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6666 Z= 0.096 Angle : 0.444 4.006 9114 Z= 0.246 Chirality : 0.038 0.120 1140 Planarity : 0.002 0.024 1218 Dihedral : 3.890 11.630 966 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -2.76 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.30 (0.37), residues: 216 loop : -2.57 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 136 TYR 0.002 0.000 TYR A 137 PHE 0.006 0.001 PHE F 54 HIS 0.001 0.000 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 6660) covalent geometry : angle 0.44205 ( 9102) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.33397 ( 12) hydrogen bonds : bond 0.02604 ( 139) hydrogen bonds : angle 5.51038 ( 312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.274 Fit side-chains REVERT: C 24 ASP cc_start: 0.9116 (t70) cc_final: 0.8075 (p0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0692 time to fit residues: 3.2784 Evaluate side-chains 16 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2734 r_free = 0.2734 target = 0.043573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.037995 restraints weight = 39314.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.039098 restraints weight = 22677.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.039852 restraints weight = 15107.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.040428 restraints weight = 11094.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.040786 restraints weight = 8640.992| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6666 Z= 0.101 Angle : 0.435 4.145 9114 Z= 0.238 Chirality : 0.038 0.120 1140 Planarity : 0.002 0.023 1218 Dihedral : 3.606 12.612 966 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -2.46 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.03 (0.37), residues: 216 loop : -2.40 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.002 0.000 TYR F 158 PHE 0.006 0.001 PHE B 133 HIS 0.002 0.000 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6660) covalent geometry : angle 0.43139 ( 9102) SS BOND : bond 0.00148 ( 6) SS BOND : angle 1.55596 ( 12) hydrogen bonds : bond 0.02313 ( 139) hydrogen bonds : angle 5.03040 ( 312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.210 Fit side-chains REVERT: E 24 ASP cc_start: 0.8844 (t0) cc_final: 0.8266 (m-30) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0515 time to fit residues: 2.3020 Evaluate side-chains 18 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2711 r_free = 0.2711 target = 0.042902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.037337 restraints weight = 40366.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038395 restraints weight = 23261.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.039118 restraints weight = 15637.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.039661 restraints weight = 11629.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.040047 restraints weight = 9162.331| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6666 Z= 0.154 Angle : 0.472 5.317 9114 Z= 0.256 Chirality : 0.038 0.118 1140 Planarity : 0.002 0.022 1218 Dihedral : 3.960 12.859 966 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -2.34 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.05 (0.35), residues: 222 loop : -2.30 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.005 0.001 TYR F 158 PHE 0.006 0.001 PHE A 133 HIS 0.001 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6660) covalent geometry : angle 0.46902 ( 9102) SS BOND : bond 0.00105 ( 6) SS BOND : angle 1.48329 ( 12) hydrogen bonds : bond 0.02795 ( 139) hydrogen bonds : angle 5.03655 ( 312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.243 Fit side-chains REVERT: B 89 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6215 (tm-30) REVERT: B 151 ASP cc_start: 0.8729 (m-30) cc_final: 0.8515 (m-30) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0445 time to fit residues: 2.0689 Evaluate side-chains 19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 58 optimal weight: 0.8980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2742 r_free = 0.2742 target = 0.043904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.038312 restraints weight = 38930.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.039411 restraints weight = 22828.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.040166 restraints weight = 15306.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.040733 restraints weight = 11285.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.041143 restraints weight = 8809.735| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6666 Z= 0.086 Angle : 0.415 4.879 9114 Z= 0.229 Chirality : 0.038 0.121 1140 Planarity : 0.002 0.019 1218 Dihedral : 3.420 13.114 966 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -2.11 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.30 (0.36), residues: 216 loop : -2.15 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 136 TYR 0.001 0.000 TYR E 158 PHE 0.006 0.001 PHE F 54 HIS 0.000 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6660) covalent geometry : angle 0.41303 ( 9102) SS BOND : bond 0.00061 ( 6) SS BOND : angle 1.29012 ( 12) hydrogen bonds : bond 0.02070 ( 139) hydrogen bonds : angle 4.74624 ( 312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.165 Fit side-chains REVERT: B 151 ASP cc_start: 0.8819 (m-30) cc_final: 0.8570 (m-30) REVERT: E 105 ASP cc_start: 0.8046 (t70) cc_final: 0.7469 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0512 time to fit residues: 2.3617 Evaluate side-chains 18 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2739 r_free = 0.2739 target = 0.043834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.038309 restraints weight = 38861.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.039391 restraints weight = 22677.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.040172 restraints weight = 15159.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.040721 restraints weight = 11077.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.041134 restraints weight = 8644.325| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6666 Z= 0.104 Angle : 0.436 4.820 9114 Z= 0.237 Chirality : 0.038 0.122 1140 Planarity : 0.002 0.020 1218 Dihedral : 3.483 11.835 966 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -2.01 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.35 (0.35), residues: 216 loop : -2.07 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.002 0.000 TYR C 158 PHE 0.005 0.001 PHE C 133 HIS 0.001 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6660) covalent geometry : angle 0.43261 ( 9102) SS BOND : bond 0.00174 ( 6) SS BOND : angle 1.47078 ( 12) hydrogen bonds : bond 0.02203 ( 139) hydrogen bonds : angle 4.65106 ( 312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.243 Fit side-chains REVERT: B 151 ASP cc_start: 0.8719 (m-30) cc_final: 0.8497 (m-30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0549 time to fit residues: 2.2609 Evaluate side-chains 17 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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 = 0.2755 r_free = 0.2755 target = 0.044432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.038877 restraints weight = 38764.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.039985 restraints weight = 22668.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.040778 restraints weight = 15119.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.041340 restraints weight = 11016.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041745 restraints weight = 8556.867| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6666 Z= 0.084 Angle : 0.417 4.718 9114 Z= 0.228 Chirality : 0.038 0.121 1140 Planarity : 0.002 0.019 1218 Dihedral : 3.349 12.612 966 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -1.91 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.41 (0.35), residues: 216 loop : -2.00 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 136 TYR 0.001 0.000 TYR E 158 PHE 0.005 0.001 PHE F 54 HIS 0.000 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 6660) covalent geometry : angle 0.41423 ( 9102) SS BOND : bond 0.00238 ( 6) SS BOND : angle 1.31171 ( 12) hydrogen bonds : bond 0.02000 ( 139) hydrogen bonds : angle 4.61490 ( 312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.288 Fit side-chains REVERT: B 151 ASP cc_start: 0.8660 (m-30) cc_final: 0.8446 (m-30) REVERT: E 24 ASP cc_start: 0.8816 (t70) cc_final: 0.8614 (t0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0525 time to fit residues: 2.5068 Evaluate side-chains 19 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 0.0770 chunk 38 optimal weight: 0.3980 chunk 12 optimal weight: 0.0870 chunk 1 optimal weight: 0.0030 overall best weight: 0.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.045909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.040064 restraints weight = 37376.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.041300 restraints weight = 21300.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042157 restraints weight = 13881.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042781 restraints weight = 9947.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.043169 restraints weight = 7550.216| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.021 6666 Z= 0.065 Angle : 0.397 4.265 9114 Z= 0.217 Chirality : 0.038 0.123 1140 Planarity : 0.002 0.019 1218 Dihedral : 2.884 9.872 966 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.07 (0.34), residues: 246 loop : -1.68 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 136 TYR 0.002 0.000 TYR D 158 PHE 0.005 0.001 PHE F 54 HIS 0.001 0.000 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00142 ( 6660) covalent geometry : angle 0.39541 ( 9102) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.15111 ( 12) hydrogen bonds : bond 0.01645 ( 139) hydrogen bonds : angle 4.27081 ( 312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.254 Fit side-chains REVERT: A 91 SER cc_start: 0.8459 (m) cc_final: 0.7992 (t) REVERT: B 151 ASP cc_start: 0.8694 (m-30) cc_final: 0.8379 (m-30) REVERT: E 105 ASP cc_start: 0.7938 (t70) cc_final: 0.7398 (p0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0592 time to fit residues: 2.9097 Evaluate side-chains 22 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.044908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.039124 restraints weight = 38167.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.040301 restraints weight = 21954.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.041120 restraints weight = 14518.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041684 restraints weight = 10555.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.042140 restraints weight = 8218.988| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6666 Z= 0.085 Angle : 0.403 4.072 9114 Z= 0.219 Chirality : 0.038 0.127 1140 Planarity : 0.002 0.019 1218 Dihedral : 3.049 10.542 966 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.60 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.13 (0.34), residues: 246 loop : -1.65 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 136 TYR 0.003 0.000 TYR C 137 PHE 0.005 0.001 PHE B 133 HIS 0.001 0.000 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6660) covalent geometry : angle 0.40083 ( 9102) SS BOND : bond 0.00160 ( 6) SS BOND : angle 1.24589 ( 12) hydrogen bonds : bond 0.01961 ( 139) hydrogen bonds : angle 4.19819 ( 312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.266 Fit side-chains REVERT: E 24 ASP cc_start: 0.8918 (t0) cc_final: 0.8467 (m-30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0612 time to fit residues: 2.7793 Evaluate side-chains 20 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.042389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.036699 restraints weight = 39823.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.037807 restraints weight = 22728.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.038584 restraints weight = 15096.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.039130 restraints weight = 11032.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.039537 restraints weight = 8598.469| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6666 Z= 0.234 Angle : 0.559 6.416 9114 Z= 0.299 Chirality : 0.038 0.121 1140 Planarity : 0.002 0.024 1218 Dihedral : 4.352 15.705 966 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.98 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.28 (0.34), residues: 216 loop : -2.01 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 136 TYR 0.006 0.001 TYR F 158 PHE 0.009 0.001 PHE A 73 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 6660) covalent geometry : angle 0.55604 ( 9102) SS BOND : bond 0.00172 ( 6) SS BOND : angle 1.71186 ( 12) hydrogen bonds : bond 0.03325 ( 139) hydrogen bonds : angle 4.85164 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.41 seconds wall clock time: 15 minutes 40.59 seconds (940.59 seconds total)