Starting phenix.real_space_refine on Sun Apr 5 14:14:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u65_63896/04_2026/9u65_63896.map" } resolution = 3.41 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= 0.029 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 54 5.16 5 C 6813 2.51 5 N 1869 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10809 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "D" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1088 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain breaks: 2 Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "E" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1088 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain breaks: 2 Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "F" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1088 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain breaks: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.21 Number of scatterers: 10809 At special positions: 0 Unit cell: (90.2, 86.92, 136.12, 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 54 16.00 O 2073 8.00 N 1869 7.00 C 6813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS E 137 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS F 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " 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: 0.82 Conformation dependent library (CDL) restraints added in 491.6 milliseconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2526 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 26.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.801A pdb=" N LEU A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.667A pdb=" N ASP A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A 69 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 removed outlier: 3.908A pdb=" N THR A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 124 removed outlier: 4.313A pdb=" N THR D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.950A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.853A pdb=" N LEU B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.755A pdb=" N ASP B 68 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 69 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 72 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 73 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 removed outlier: 3.921A pdb=" N THR B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'E' and resid 37 through 58 Processing helix chain 'E' and resid 74 through 124 removed outlier: 4.307A pdb=" N THR E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.965A pdb=" N MET E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS E 153 " --> pdb=" O MET E 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.814A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.706A pdb=" N ASP C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU C 69 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR C 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 73 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 removed outlier: 3.933A pdb=" N THR C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.563A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 124 removed outlier: 4.329A pdb=" N THR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.934A pdb=" N MET F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS F 153 " --> pdb=" O MET F 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.979A pdb=" N ASP A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.872A pdb=" N VAL A 30 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 314 " --> pdb=" O VAL A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 removed outlier: 7.961A pdb=" N LEU A 41 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR A 277 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER A 43 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.379A pdb=" N ILE A 79 " --> pdb=" O MET A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 115 removed outlier: 3.760A pdb=" N SER A 110 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 258 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N HIS A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE A 176 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 115 removed outlier: 3.760A pdb=" N SER A 110 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 258 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N HIS A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE A 176 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 138 removed outlier: 4.620A pdb=" N CYS A 136 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 143 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AA9, first strand: chain 'A' and resid 279 through 280 removed outlier: 3.693A pdb=" N CYS A 279 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 16 removed outlier: 4.078A pdb=" N ASP B 14 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.889A pdb=" N LEU B 41 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR B 277 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B 43 " --> pdb=" O THR B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.605A pdb=" N ILE B 80 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE B 79 " --> pdb=" O MET B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 108 through 115 removed outlier: 3.767A pdb=" N SER B 110 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 258 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS B 253 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE B 176 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 133 through 138 removed outlier: 4.608A pdb=" N CYS B 136 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 143 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'B' and resid 161 through 166 Processing sheet with id=AB9, first strand: chain 'B' and resid 279 through 280 removed outlier: 3.697A pdb=" N CYS B 279 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.017A pdb=" N ASP C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.916A pdb=" N LEU C 41 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR C 277 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER C 43 " --> pdb=" O THR C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.352A pdb=" N ILE C 79 " --> pdb=" O MET C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 108 through 115 removed outlier: 3.758A pdb=" N SER C 110 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 258 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS C 253 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE C 176 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 133 through 138 removed outlier: 4.635A pdb=" N CYS C 136 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 143 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AC8, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AC9, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.715A pdb=" N CYS C 279 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 292 through 293 387 hydrogen bonds defined for protein. 1080 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: 1.64 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1806 1.31 - 1.44: 3072 1.44 - 1.57: 6105 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 11055 Sorted by residual: bond pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.83e+01 bond pdb=" C PRO C 183 " pdb=" O PRO C 183 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C PRO C 182 " pdb=" O PRO C 182 " ideal model delta sigma weight residual 1.246 1.218 0.028 8.50e-03 1.38e+04 1.07e+01 bond pdb=" C ARG D 76 " pdb=" N MET D 77 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.36e-02 5.41e+03 4.53e+00 bond pdb=" N PRO C 182 " pdb=" CD PRO C 182 " ideal model delta sigma weight residual 1.473 1.446 0.027 1.40e-02 5.10e+03 3.79e+00 ... (remaining 11050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 14575 1.71 - 3.43: 334 3.43 - 5.14: 41 5.14 - 6.86: 20 6.86 - 8.57: 9 Bond angle restraints: 14979 Sorted by residual: angle pdb=" N MET D 77 " pdb=" CA MET D 77 " pdb=" C MET D 77 " ideal model delta sigma weight residual 111.36 105.90 5.46 1.09e+00 8.42e-01 2.51e+01 angle pdb=" C ARG D 76 " pdb=" N MET D 77 " pdb=" CA MET D 77 " ideal model delta sigma weight residual 120.29 113.52 6.77 1.42e+00 4.96e-01 2.27e+01 angle pdb=" C THR C 184 " pdb=" CA THR C 184 " pdb=" CB THR C 184 " ideal model delta sigma weight residual 110.95 102.38 8.57 1.80e+00 3.09e-01 2.27e+01 angle pdb=" CA GLU E 57 " pdb=" CB GLU E 57 " pdb=" CG GLU E 57 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" N GLU E 57 " pdb=" CA GLU E 57 " pdb=" C GLU E 57 " ideal model delta sigma weight residual 110.44 115.40 -4.96 1.20e+00 6.94e-01 1.71e+01 ... (remaining 14974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5860 15.74 - 31.49: 528 31.49 - 47.23: 128 47.23 - 62.97: 45 62.97 - 78.71: 9 Dihedral angle restraints: 6570 sinusoidal: 2634 harmonic: 3936 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -31.32 -54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " pdb=" SG CYS E 137 " pdb=" CB CYS E 137 " ideal model delta sinusoidal sigma weight residual -86.00 -31.58 -54.42 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS C 4 " pdb=" SG CYS C 4 " pdb=" SG CYS F 137 " pdb=" CB CYS F 137 " ideal model delta sinusoidal sigma weight residual -86.00 -32.07 -53.93 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 6567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1225 0.045 - 0.089: 298 0.089 - 0.134: 96 0.134 - 0.179: 15 0.179 - 0.224: 4 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CB THR C 184 " pdb=" CA THR C 184 " pdb=" OG1 THR C 184 " pdb=" CG2 THR C 184 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA HIS C 181 " pdb=" N HIS C 181 " pdb=" C HIS C 181 " pdb=" CB HIS C 181 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA THR C 184 " pdb=" N THR C 184 " pdb=" C THR C 184 " pdb=" CB THR C 184 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1635 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 290 " -0.095 5.00e-02 4.00e+02 1.41e-01 3.19e+01 pdb=" N PRO C 291 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 290 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 291 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 290 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 291 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.046 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1165 2.75 - 3.29: 10415 3.29 - 3.83: 17691 3.83 - 4.36: 19929 4.36 - 4.90: 34965 Nonbonded interactions: 84165 Sorted by model distance: nonbonded pdb=" O GLY C 53 " pdb=" OG SER C 85 " model vdw 2.214 3.040 nonbonded pdb=" O GLY B 53 " pdb=" OG SER B 85 " model vdw 2.217 3.040 nonbonded pdb=" O PRO A 118 " pdb=" OG SER A 122 " model vdw 2.222 3.040 nonbonded pdb=" O PRO B 118 " pdb=" OG SER B 122 " model vdw 2.228 3.040 nonbonded pdb=" O GLY A 53 " pdb=" OG SER A 85 " model vdw 2.232 3.040 ... (remaining 84160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.480 Find NCS groups from input model: 0.120 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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 0.059 11070 Z= 0.173 Angle : 0.659 8.574 15009 Z= 0.361 Chirality : 0.045 0.224 1638 Planarity : 0.006 0.141 1920 Dihedral : 13.493 78.714 3999 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.17 % Allowed : 0.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1338 helix: 0.38 (0.27), residues: 333 sheet: 0.75 (0.37), residues: 225 loop : -1.51 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.020 0.001 TYR B 207 PHE 0.016 0.002 PHE D 70 TRP 0.017 0.001 TRP A 252 HIS 0.005 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00336 (11055) covalent geometry : angle 0.65696 (14979) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.34173 ( 30) hydrogen bonds : bond 0.11621 ( 379) hydrogen bonds : angle 6.16950 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8184 (tptt) cc_final: 0.7955 (tptp) REVERT: A 278 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7508 (mtmm) REVERT: B 23 ASN cc_start: 0.6916 (t0) cc_final: 0.6678 (p0) REVERT: B 77 SER cc_start: 0.7222 (m) cc_final: 0.6577 (p) REVERT: B 156 ASN cc_start: 0.7390 (t0) cc_final: 0.7162 (t0) REVERT: B 245 THR cc_start: 0.8018 (t) cc_final: 0.7813 (m) REVERT: E 97 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6667 (mm-30) REVERT: C 156 ASN cc_start: 0.6746 (t0) cc_final: 0.6419 (t0) REVERT: C 184 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7300 (p) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.1381 time to fit residues: 33.6976 Evaluate side-chains 164 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain C residue 184 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 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 87 ASN D 79 ASN E 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145623 restraints weight = 15688.981| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.17 r_work: 0.3726 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 11070 Z= 0.431 Angle : 0.836 10.641 15009 Z= 0.443 Chirality : 0.053 0.220 1638 Planarity : 0.007 0.085 1920 Dihedral : 6.194 54.193 1453 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.41 % Allowed : 7.46 % Favored : 91.13 % 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: -1.55 (0.21), residues: 1338 helix: -0.35 (0.27), residues: 342 sheet: 0.19 (0.36), residues: 222 loop : -1.78 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 130 TYR 0.033 0.004 TYR B 158 PHE 0.027 0.003 PHE B 210 TRP 0.025 0.003 TRP A 231 HIS 0.019 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00959 (11055) covalent geometry : angle 0.83432 (14979) SS BOND : bond 0.00521 ( 15) SS BOND : angle 1.36782 ( 30) hydrogen bonds : bond 0.06264 ( 379) hydrogen bonds : angle 5.79253 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.407 Fit side-chains REVERT: A 41 LEU cc_start: 0.7087 (mp) cc_final: 0.6819 (mt) REVERT: D 74 GLU cc_start: 0.7560 (tt0) cc_final: 0.7068 (tt0) REVERT: D 79 ASN cc_start: 0.8511 (m-40) cc_final: 0.8236 (m110) REVERT: D 97 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7072 (mt-10) REVERT: E 75 LYS cc_start: 0.8394 (tptm) cc_final: 0.8014 (tptp) REVERT: E 78 GLU cc_start: 0.7929 (tp30) cc_final: 0.7437 (tp30) REVERT: E 79 ASN cc_start: 0.8598 (m-40) cc_final: 0.8284 (m110) REVERT: E 97 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6951 (mm-30) REVERT: E 114 ASN cc_start: 0.6260 (m110) cc_final: 0.5993 (m110) REVERT: C 156 ASN cc_start: 0.7244 (t0) cc_final: 0.6971 (t0) REVERT: C 184 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (p) REVERT: C 208 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7101 (ttmm) REVERT: F 74 GLU cc_start: 0.7551 (tt0) cc_final: 0.6892 (tt0) REVERT: F 77 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7474 (mtt) REVERT: F 114 ASN cc_start: 0.6588 (m110) cc_final: 0.6368 (m110) outliers start: 17 outliers final: 8 residues processed: 186 average time/residue: 0.1239 time to fit residues: 31.3838 Evaluate side-chains 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 146 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 93 optimal weight: 0.0770 chunk 115 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 114 ASN E 81 ASN C 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154388 restraints weight = 15664.098| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.10 r_work: 0.3844 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11070 Z= 0.138 Angle : 0.586 8.744 15009 Z= 0.308 Chirality : 0.043 0.187 1638 Planarity : 0.005 0.063 1920 Dihedral : 5.045 35.790 1450 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.66 % Allowed : 11.11 % Favored : 88.23 % 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: -1.15 (0.22), residues: 1338 helix: 0.04 (0.27), residues: 342 sheet: 0.55 (0.37), residues: 210 loop : -1.57 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 113 TYR 0.039 0.001 TYR B 229 PHE 0.011 0.001 PHE B 111 TRP 0.008 0.001 TRP C 231 HIS 0.006 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00288 (11055) covalent geometry : angle 0.58619 (14979) SS BOND : bond 0.00342 ( 15) SS BOND : angle 0.34712 ( 30) hydrogen bonds : bond 0.04776 ( 379) hydrogen bonds : angle 5.46348 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: D 74 GLU cc_start: 0.7384 (tt0) cc_final: 0.6961 (tt0) REVERT: D 79 ASN cc_start: 0.8405 (m-40) cc_final: 0.8146 (m110) REVERT: D 97 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7217 (mt-10) REVERT: B 38 ASN cc_start: 0.7456 (p0) cc_final: 0.7203 (p0) REVERT: B 87 ASN cc_start: 0.7548 (t0) cc_final: 0.7343 (t0) REVERT: E 79 ASN cc_start: 0.8455 (m-40) cc_final: 0.8204 (m-40) REVERT: E 97 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6958 (mm-30) REVERT: E 114 ASN cc_start: 0.5982 (m110) cc_final: 0.5748 (m110) REVERT: C 156 ASN cc_start: 0.7127 (t0) cc_final: 0.6831 (t0) REVERT: C 184 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7502 (p) REVERT: F 74 GLU cc_start: 0.7430 (tt0) cc_final: 0.7156 (tt0) REVERT: F 77 MET cc_start: 0.7625 (mmm) cc_final: 0.7412 (mtt) outliers start: 8 outliers final: 5 residues processed: 176 average time/residue: 0.1363 time to fit residues: 32.1452 Evaluate side-chains 168 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 0.0000 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 196 ASN E 81 ASN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.174706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152876 restraints weight = 15760.911| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.12 r_work: 0.3832 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11070 Z= 0.154 Angle : 0.578 11.076 15009 Z= 0.300 Chirality : 0.043 0.191 1638 Planarity : 0.004 0.060 1920 Dihedral : 4.842 30.829 1450 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.41 % Allowed : 12.19 % Favored : 86.40 % 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: -1.02 (0.22), residues: 1338 helix: 0.23 (0.28), residues: 342 sheet: 0.57 (0.37), residues: 225 loop : -1.55 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.024 0.001 TYR B 229 PHE 0.011 0.001 PHE B 111 TRP 0.008 0.001 TRP A 252 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00331 (11055) covalent geometry : angle 0.57805 (14979) SS BOND : bond 0.00274 ( 15) SS BOND : angle 0.43539 ( 30) hydrogen bonds : bond 0.04622 ( 379) hydrogen bonds : angle 5.34408 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8497 (tppt) cc_final: 0.8177 (tptp) REVERT: D 74 GLU cc_start: 0.7414 (tt0) cc_final: 0.6919 (tt0) REVERT: D 79 ASN cc_start: 0.8412 (m-40) cc_final: 0.8115 (m110) REVERT: E 79 ASN cc_start: 0.8440 (m-40) cc_final: 0.8207 (m-40) REVERT: E 97 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6984 (mm-30) REVERT: C 156 ASN cc_start: 0.7132 (t0) cc_final: 0.6834 (t0) REVERT: C 184 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 287 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8203 (mmmm) REVERT: F 74 GLU cc_start: 0.7434 (tt0) cc_final: 0.7133 (tt0) REVERT: F 77 MET cc_start: 0.7703 (mmm) cc_final: 0.7364 (mtt) outliers start: 17 outliers final: 12 residues processed: 178 average time/residue: 0.1336 time to fit residues: 31.7566 Evaluate side-chains 177 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN E 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.173840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152463 restraints weight = 15664.167| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.03 r_work: 0.3831 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11070 Z= 0.191 Angle : 0.616 12.298 15009 Z= 0.317 Chirality : 0.044 0.190 1638 Planarity : 0.005 0.060 1920 Dihedral : 4.883 25.627 1450 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.82 % Allowed : 13.93 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.04 (0.22), residues: 1338 helix: 0.22 (0.28), residues: 342 sheet: 0.50 (0.38), residues: 225 loop : -1.54 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.019 0.002 TYR B 229 PHE 0.011 0.002 PHE C 95 TRP 0.008 0.001 TRP A 76 HIS 0.010 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00416 (11055) covalent geometry : angle 0.61580 (14979) SS BOND : bond 0.00293 ( 15) SS BOND : angle 0.56939 ( 30) hydrogen bonds : bond 0.04799 ( 379) hydrogen bonds : angle 5.34185 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 41 LEU cc_start: 0.7114 (mp) cc_final: 0.6871 (mt) REVERT: A 163 LYS cc_start: 0.8503 (tppt) cc_final: 0.8188 (tptp) REVERT: A 236 GLN cc_start: 0.8208 (mp10) cc_final: 0.8003 (mp10) REVERT: A 290 LEU cc_start: 0.8014 (mt) cc_final: 0.7711 (mt) REVERT: D 79 ASN cc_start: 0.8448 (m-40) cc_final: 0.8155 (m110) REVERT: E 74 GLU cc_start: 0.7466 (tt0) cc_final: 0.7210 (tp30) REVERT: E 75 LYS cc_start: 0.8347 (tptm) cc_final: 0.8121 (tppt) REVERT: E 114 ASN cc_start: 0.6037 (m110) cc_final: 0.5808 (m110) REVERT: C 156 ASN cc_start: 0.7140 (t0) cc_final: 0.6840 (t0) REVERT: F 74 GLU cc_start: 0.7486 (tt0) cc_final: 0.7143 (tt0) REVERT: F 77 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7370 (mtt) outliers start: 22 outliers final: 14 residues processed: 189 average time/residue: 0.1310 time to fit residues: 33.0735 Evaluate side-chains 189 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain F residue 77 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.0010 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153921 restraints weight = 15686.547| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.05 r_work: 0.3851 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11070 Z= 0.135 Angle : 0.589 16.023 15009 Z= 0.299 Chirality : 0.043 0.186 1638 Planarity : 0.004 0.058 1920 Dihedral : 4.641 20.264 1449 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.07 % Allowed : 14.93 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1338 helix: 0.27 (0.28), residues: 342 sheet: 0.53 (0.38), residues: 225 loop : -1.43 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 146 TYR 0.021 0.001 TYR A 145 PHE 0.013 0.001 PHE B 111 TRP 0.005 0.001 TRP D 14 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00289 (11055) covalent geometry : angle 0.58925 (14979) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.50853 ( 30) hydrogen bonds : bond 0.04462 ( 379) hydrogen bonds : angle 5.29901 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.7575 (p) cc_final: 0.7302 (p) REVERT: A 163 LYS cc_start: 0.8492 (tppt) cc_final: 0.8179 (tptp) REVERT: A 290 LEU cc_start: 0.7988 (mt) cc_final: 0.7710 (mt) REVERT: D 17 MET cc_start: 0.1492 (OUTLIER) cc_final: 0.1274 (mtp) REVERT: D 59 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7036 (pmm) REVERT: C 156 ASN cc_start: 0.7127 (t0) cc_final: 0.6820 (t0) REVERT: F 74 GLU cc_start: 0.7426 (tt0) cc_final: 0.6998 (tt0) REVERT: F 77 MET cc_start: 0.7679 (mmm) cc_final: 0.7150 (mtt) outliers start: 25 outliers final: 12 residues processed: 188 average time/residue: 0.1324 time to fit residues: 33.4838 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 171 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153841 restraints weight = 15707.290| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.07 r_work: 0.3846 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11070 Z= 0.148 Angle : 0.596 14.210 15009 Z= 0.302 Chirality : 0.043 0.184 1638 Planarity : 0.004 0.058 1920 Dihedral : 4.631 20.164 1449 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 16.17 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1338 helix: 0.28 (0.28), residues: 342 sheet: 0.54 (0.39), residues: 210 loop : -1.37 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 313 TYR 0.017 0.001 TYR C 306 PHE 0.012 0.001 PHE B 111 TRP 0.013 0.001 TRP A 252 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00323 (11055) covalent geometry : angle 0.59605 (14979) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.50423 ( 30) hydrogen bonds : bond 0.04379 ( 379) hydrogen bonds : angle 5.27518 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.7587 (p) cc_final: 0.7325 (p) REVERT: A 163 LYS cc_start: 0.8483 (tppt) cc_final: 0.8186 (tptp) REVERT: A 290 LEU cc_start: 0.8015 (mt) cc_final: 0.7729 (mt) REVERT: D 17 MET cc_start: 0.1631 (OUTLIER) cc_final: 0.1396 (mtp) REVERT: D 59 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.7062 (pmm) REVERT: D 74 GLU cc_start: 0.7382 (tt0) cc_final: 0.7069 (tt0) REVERT: D 79 ASN cc_start: 0.8335 (m-40) cc_final: 0.8131 (m110) REVERT: C 156 ASN cc_start: 0.7119 (t0) cc_final: 0.6816 (t0) REVERT: F 74 GLU cc_start: 0.7471 (tt0) cc_final: 0.7132 (tt0) REVERT: F 77 MET cc_start: 0.7531 (mmm) cc_final: 0.7089 (mtt) outliers start: 17 outliers final: 11 residues processed: 190 average time/residue: 0.1334 time to fit residues: 33.9633 Evaluate side-chains 193 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 0.0050 chunk 111 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN E 79 ASN E 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.176225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154972 restraints weight = 15686.568| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.07 r_work: 0.3866 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11070 Z= 0.114 Angle : 0.569 12.518 15009 Z= 0.289 Chirality : 0.042 0.176 1638 Planarity : 0.004 0.056 1920 Dihedral : 4.455 20.195 1449 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.58 % Allowed : 16.50 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1338 helix: 0.44 (0.28), residues: 342 sheet: 0.51 (0.39), residues: 210 loop : -1.30 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 313 TYR 0.020 0.001 TYR C 306 PHE 0.011 0.001 PHE B 111 TRP 0.012 0.001 TRP A 252 HIS 0.004 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00249 (11055) covalent geometry : angle 0.56951 (14979) SS BOND : bond 0.00211 ( 15) SS BOND : angle 0.48479 ( 30) hydrogen bonds : bond 0.04056 ( 379) hydrogen bonds : angle 5.18196 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.7516 (p) cc_final: 0.7277 (p) REVERT: A 54 ASN cc_start: 0.7925 (m-40) cc_final: 0.7720 (m-40) REVERT: A 163 LYS cc_start: 0.8472 (tppt) cc_final: 0.8174 (tptp) REVERT: A 208 LYS cc_start: 0.7546 (tppt) cc_final: 0.7192 (tppt) REVERT: A 287 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8286 (mptm) REVERT: D 59 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7057 (pmm) REVERT: D 74 GLU cc_start: 0.7309 (tt0) cc_final: 0.6987 (tt0) REVERT: B 29 SER cc_start: 0.7566 (p) cc_final: 0.7241 (p) REVERT: C 156 ASN cc_start: 0.7104 (t0) cc_final: 0.6802 (t0) REVERT: C 208 LYS cc_start: 0.7494 (ttmm) cc_final: 0.6804 (ttmm) REVERT: C 258 LYS cc_start: 0.8162 (mttp) cc_final: 0.7935 (mttp) REVERT: F 74 GLU cc_start: 0.7484 (tt0) cc_final: 0.7110 (tt0) REVERT: F 77 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7020 (mtt) outliers start: 19 outliers final: 10 residues processed: 192 average time/residue: 0.1304 time to fit residues: 33.7514 Evaluate side-chains 194 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain F residue 77 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 120 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.178037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157052 restraints weight = 15537.798| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.09 r_work: 0.3873 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11070 Z= 0.109 Angle : 0.558 11.197 15009 Z= 0.285 Chirality : 0.042 0.169 1638 Planarity : 0.004 0.057 1920 Dihedral : 4.369 19.944 1449 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.58 % Allowed : 17.00 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1338 helix: 0.59 (0.29), residues: 342 sheet: 0.03 (0.41), residues: 180 loop : -1.18 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.021 0.001 TYR C 306 PHE 0.009 0.001 PHE B 111 TRP 0.010 0.001 TRP A 252 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00237 (11055) covalent geometry : angle 0.55772 (14979) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.48052 ( 30) hydrogen bonds : bond 0.03864 ( 379) hydrogen bonds : angle 5.09695 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.7560 (p) cc_final: 0.7326 (p) REVERT: A 54 ASN cc_start: 0.7886 (m-40) cc_final: 0.7676 (m-40) REVERT: A 163 LYS cc_start: 0.8456 (tppt) cc_final: 0.8160 (tptp) REVERT: A 208 LYS cc_start: 0.7531 (tppt) cc_final: 0.7171 (tppt) REVERT: A 287 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8246 (mptm) REVERT: D 17 MET cc_start: 0.1492 (OUTLIER) cc_final: 0.1234 (mtp) REVERT: D 59 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7079 (pmm) REVERT: D 74 GLU cc_start: 0.7343 (tt0) cc_final: 0.6883 (tt0) REVERT: B 29 SER cc_start: 0.7537 (p) cc_final: 0.7214 (p) REVERT: C 41 LEU cc_start: 0.7285 (mt) cc_final: 0.7058 (mp) REVERT: C 156 ASN cc_start: 0.7087 (t0) cc_final: 0.6853 (t0) REVERT: C 208 LYS cc_start: 0.7478 (ttmm) cc_final: 0.6755 (ttmm) REVERT: C 258 LYS cc_start: 0.8158 (mttp) cc_final: 0.7929 (mttp) outliers start: 19 outliers final: 12 residues processed: 188 average time/residue: 0.1356 time to fit residues: 34.1250 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 308 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 ASN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.175298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154125 restraints weight = 15579.376| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.07 r_work: 0.3846 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11070 Z= 0.170 Angle : 0.602 11.194 15009 Z= 0.309 Chirality : 0.043 0.201 1638 Planarity : 0.004 0.058 1920 Dihedral : 4.564 20.738 1449 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 17.33 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1338 helix: 0.44 (0.28), residues: 342 sheet: 0.45 (0.39), residues: 210 loop : -1.29 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 130 TYR 0.018 0.001 TYR C 306 PHE 0.015 0.001 PHE B 111 TRP 0.011 0.001 TRP A 252 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00374 (11055) covalent geometry : angle 0.60189 (14979) SS BOND : bond 0.00253 ( 15) SS BOND : angle 0.52502 ( 30) hydrogen bonds : bond 0.04253 ( 379) hydrogen bonds : angle 5.13842 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.7621 (p) cc_final: 0.7369 (p) REVERT: A 163 LYS cc_start: 0.8480 (tppt) cc_final: 0.8187 (tptp) REVERT: A 227 MET cc_start: 0.6439 (ptt) cc_final: 0.6043 (ptt) REVERT: A 287 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8296 (mptm) REVERT: D 17 MET cc_start: 0.1577 (OUTLIER) cc_final: 0.1372 (mtp) REVERT: D 59 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6982 (pmm) REVERT: D 74 GLU cc_start: 0.7490 (tt0) cc_final: 0.6938 (tt0) REVERT: D 77 MET cc_start: 0.7806 (mtp) cc_final: 0.7366 (mtt) REVERT: D 79 ASN cc_start: 0.8351 (m-40) cc_final: 0.8112 (m110) REVERT: B 29 SER cc_start: 0.7662 (p) cc_final: 0.7334 (p) REVERT: C 41 LEU cc_start: 0.7407 (mt) cc_final: 0.7141 (mp) REVERT: C 130 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6992 (mtm110) REVERT: C 156 ASN cc_start: 0.7116 (t0) cc_final: 0.6878 (t0) REVERT: C 208 LYS cc_start: 0.7573 (ttmm) cc_final: 0.6856 (ttmm) outliers start: 17 outliers final: 10 residues processed: 189 average time/residue: 0.1365 time to fit residues: 34.6119 Evaluate side-chains 194 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 chunk 118 optimal weight: 0.2980 chunk 108 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.176500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155133 restraints weight = 15679.687| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.17 r_work: 0.3850 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11070 Z= 0.134 Angle : 0.599 15.537 15009 Z= 0.306 Chirality : 0.043 0.173 1638 Planarity : 0.004 0.057 1920 Dihedral : 4.497 21.102 1449 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.16 % Allowed : 17.91 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1338 helix: 0.45 (0.28), residues: 342 sheet: 0.43 (0.39), residues: 210 loop : -1.26 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 130 TYR 0.020 0.001 TYR C 306 PHE 0.014 0.001 PHE B 111 TRP 0.009 0.001 TRP A 252 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00298 (11055) covalent geometry : angle 0.59951 (14979) SS BOND : bond 0.00219 ( 15) SS BOND : angle 0.42333 ( 30) hydrogen bonds : bond 0.04089 ( 379) hydrogen bonds : angle 5.14082 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.83 seconds wall clock time: 39 minutes 39.95 seconds (2379.95 seconds total)