Starting phenix.real_space_refine on Tue Feb 11 19:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5oh0_3809/02_2025/5oh0_3809_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oh0_3809/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5oh0_3809/02_2025/5oh0_3809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oh0_3809/02_2025/5oh0_3809.map" model { file = "/net/cci-nas-00/data/ceres_data/5oh0_3809/02_2025/5oh0_3809_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oh0_3809/02_2025/5oh0_3809_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, F Time building chain proxies: 2.70, per 1000 atoms: 0.41 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.73 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: 1.40 Time building geometry restraints manager: 1.84 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: 131 28.57 - 42.85: 20 42.85 - 57.13: 0 57.13 - 71.42: 6 Dihedral angle restraints: 3867 sinusoidal: 1227 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 3864 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: 2.03 - 2.60: 53 2.60 - 3.18: 5070 3.18 - 3.75: 9234 3.75 - 4.33: 11887 4.33 - 4.90: 20810 Nonbonded interactions: 47054 Sorted by model distance: nonbonded pdb=" SG CYS F 21 " pdb=" SG CYS F 61 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 21 " pdb=" SG CYS C 61 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 21 " pdb=" SG CYS D 61 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 21 " pdb=" SG CYS E 61 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 21 " pdb=" SG CYS B 61 " model vdw 2.030 3.760 ... (remaining 47049 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.110 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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 6660 Z= 0.215 Angle : 0.750 5.312 9102 Z= 0.463 Chirality : 0.047 0.148 1140 Planarity : 0.004 0.039 1218 Dihedral : 8.942 71.416 2172 Min Nonbonded Distance : 2.029 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS B 11 PHE 0.020 0.002 PHE E 154 TYR 0.002 0.001 TYR F 158 ARG 0.001 0.000 ARG A 106 *********************** 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 : 0.738 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: 0.2056 time to fit residues: 22.0798 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 20.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** 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 = 0.2732 r_free = 0.2732 target = 0.043081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.037473 restraints weight = 38545.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.038611 restraints weight = 22167.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.039399 restraints weight = 14616.214| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6660 Z= 0.245 Angle : 0.508 5.500 9102 Z= 0.279 Chirality : 0.039 0.126 1140 Planarity : 0.003 0.031 1218 Dihedral : 4.257 12.525 966 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.25), residues: 930 helix: None (None), residues: 0 sheet: -0.95 (0.35), residues: 240 loop : -2.60 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 11 PHE 0.009 0.001 PHE A 73 TYR 0.005 0.001 TYR E 158 ARG 0.002 0.001 ARG A 136 *********************** 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 34 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.575 Fit side-chains REVERT: B 15 GLU cc_start: 0.8396 (tp30) cc_final: 0.7963 (tp30) REVERT: C 33 GLN cc_start: 0.8829 (mp10) cc_final: 0.8604 (mp10) REVERT: C 105 ASP cc_start: 0.8027 (t70) cc_final: 0.7715 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1292 time to fit residues: 7.2662 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 : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0010 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 overall best weight: 2.0150 ------------------------------------------------------------------------------- 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 129 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** 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 = 0.2723 r_free = 0.2723 target = 0.043230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.037823 restraints weight = 39426.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.038885 restraints weight = 22615.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.039647 restraints weight = 15004.926| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6660 Z= 0.190 Angle : 0.450 4.816 9102 Z= 0.248 Chirality : 0.037 0.115 1140 Planarity : 0.002 0.025 1218 Dihedral : 3.840 11.342 966 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.29 (0.38), residues: 216 loop : -2.56 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 11 PHE 0.007 0.001 PHE D 154 TYR 0.003 0.000 TYR E 158 ARG 0.002 0.000 ARG A 136 *********************** 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 28 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1486 time to fit residues: 6.6696 Evaluate side-chains 15 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- 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 125 ASN ** 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** F 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.040841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.035393 restraints weight = 40979.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.036402 restraints weight = 23523.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.037106 restraints weight = 15794.763| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 6660 Z= 0.534 Angle : 0.694 9.580 9102 Z= 0.368 Chirality : 0.041 0.115 1140 Planarity : 0.003 0.027 1218 Dihedral : 5.368 18.914 966 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.46 (0.36), residues: 222 loop : -2.57 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 11 PHE 0.013 0.002 PHE A 73 TYR 0.010 0.001 TYR F 158 ARG 0.003 0.001 ARG D 136 *********************** 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 22 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.671 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1243 time to fit residues: 4.8819 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.2676 r_free = 0.2676 target = 0.041730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.036274 restraints weight = 40320.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037336 restraints weight = 23060.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.038075 restraints weight = 15371.460| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6660 Z= 0.343 Angle : 0.562 7.304 9102 Z= 0.301 Chirality : 0.038 0.117 1140 Planarity : 0.002 0.021 1218 Dihedral : 4.770 17.145 966 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.19 (0.36), residues: 216 loop : -2.43 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 11 PHE 0.007 0.001 PHE C 133 TYR 0.006 0.001 TYR C 158 ARG 0.003 0.001 ARG A 136 *********************** 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 25 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1411 time to fit residues: 5.8550 Evaluate side-chains 15 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.2703 r_free = 0.2703 target = 0.042647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.037140 restraints weight = 39662.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.038212 restraints weight = 22728.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.038979 restraints weight = 15152.542| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6660 Z= 0.204 Angle : 0.473 5.572 9102 Z= 0.258 Chirality : 0.038 0.119 1140 Planarity : 0.002 0.020 1218 Dihedral : 4.102 14.833 966 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.01 (0.36), residues: 216 loop : -2.28 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 11 PHE 0.006 0.001 PHE C 133 TYR 0.003 0.001 TYR C 158 ARG 0.002 0.000 ARG A 136 *********************** 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 28 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.796 Fit side-chains REVERT: F 74 LEU cc_start: 0.9333 (tp) cc_final: 0.9130 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1406 time to fit residues: 6.4264 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 : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 0.0670 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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 = 0.2661 r_free = 0.2661 target = 0.041340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.035972 restraints weight = 40689.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.037000 restraints weight = 23527.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.037724 restraints weight = 15797.492| |-----------------------------------------------------------------------------| r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 6660 Z= 0.445 Angle : 0.631 8.188 9102 Z= 0.335 Chirality : 0.040 0.123 1140 Planarity : 0.003 0.023 1218 Dihedral : 5.048 18.872 966 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.21 (0.35), residues: 216 loop : -2.34 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 11 PHE 0.010 0.002 PHE C 133 TYR 0.011 0.001 TYR C 158 ARG 0.004 0.001 ARG A 136 *********************** 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 : 0.741 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1368 time to fit residues: 5.6472 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 : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.2675 r_free = 0.2675 target = 0.041812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.036359 restraints weight = 40238.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.037419 restraints weight = 23292.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.038157 restraints weight = 15591.474| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 6660 Z= 0.376 Angle : 0.579 6.868 9102 Z= 0.311 Chirality : 0.039 0.117 1140 Planarity : 0.002 0.021 1218 Dihedral : 4.839 18.447 966 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.36 (0.34), residues: 222 loop : -2.31 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 11 PHE 0.008 0.001 PHE F 154 TYR 0.008 0.001 TYR C 158 ARG 0.003 0.001 ARG A 136 *********************** 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 26 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.707 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1209 time to fit residues: 5.6160 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 : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2688 r_free = 0.2688 target = 0.042108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036643 restraints weight = 40969.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.037724 restraints weight = 23639.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.038449 restraints weight = 15793.012| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6660 Z= 0.312 Angle : 0.546 6.102 9102 Z= 0.293 Chirality : 0.039 0.118 1140 Planarity : 0.002 0.021 1218 Dihedral : 4.601 17.004 966 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.30 (0.34), residues: 222 loop : -2.28 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 11 PHE 0.008 0.001 PHE F 154 TYR 0.007 0.001 TYR C 158 ARG 0.003 0.001 ARG A 136 *********************** 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 25 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.766 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1210 time to fit residues: 5.3684 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 : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.041260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.035863 restraints weight = 42096.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.036908 restraints weight = 24200.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.037626 restraints weight = 16154.178| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 6660 Z= 0.523 Angle : 0.694 8.627 9102 Z= 0.367 Chirality : 0.041 0.133 1140 Planarity : 0.003 0.025 1218 Dihedral : 5.483 22.014 966 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.69 (0.33), residues: 246 loop : -2.29 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 11 PHE 0.012 0.002 PHE A 73 TYR 0.013 0.002 TYR C 158 ARG 0.005 0.001 ARG A 136 ********************** 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 23 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.741 Fit side-chains REVERT: E 105 ASP cc_start: 0.8109 (t70) cc_final: 0.7749 (p0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1443 time to fit residues: 5.5564 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 : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.2700 r_free = 0.2700 target = 0.042541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.037017 restraints weight = 40775.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.038108 restraints weight = 23380.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.038870 restraints weight = 15480.409| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6660 Z= 0.228 Angle : 0.509 5.339 9102 Z= 0.275 Chirality : 0.039 0.119 1140 Planarity : 0.002 0.019 1218 Dihedral : 4.410 16.241 966 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.25), residues: 930 helix: None (None), residues: 0 sheet: -0.29 (0.34), residues: 222 loop : -2.28 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 82 PHE 0.008 0.001 PHE F 154 TYR 0.004 0.001 TYR C 158 ARG 0.002 0.000 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.84 seconds wall clock time: 28 minutes 24.93 seconds (1704.93 seconds total)