Starting phenix.real_space_refine on Wed Aug 5 06:54:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265.map" model { file = "/net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p4f_71265/08_2026/9p4f_71265_neut.cif" } resolution = 3.01 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= 0.022 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 34 5.16 5 C 5446 2.51 5 N 1460 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8656 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 111} bond proxies already assigned to first conformer: 975 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1658 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain: "D" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 111} bond proxies already assigned to first conformer: 975 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1658 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 12, 'TRANS': 216} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 119 " occ=0.54 ... (10 atoms not shown) pdb=" OG BSER A 119 " occ=0.46 residue: pdb=" N ASER D 119 " occ=0.54 ... (10 atoms not shown) pdb=" OG BSER D 119 " occ=0.46 Time building chain proxies: 2.10, per 1000 atoms: 0.24 Number of scatterers: 8656 At special positions: 0 Unit cell: (202.71, 71.34, 81.78, 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 34 16.00 O 1716 8.00 N 1460 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " 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: 0.47 Conformation dependent library (CDL) restraints added in 434.8 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 28 sheets defined 5.6% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.668A pdb=" N ASP A 104 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 105 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.591A pdb=" N TYR B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.697A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.787A pdb=" N GLY C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.667A pdb=" N ASP D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 105 " --> pdb=" O VAL D 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 101 through 105' Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.591A pdb=" N TYR E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.697A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 200 removed outlier: 3.787A pdb=" N GLY F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.804A pdb=" N VAL A 12 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 37 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 115 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE A 35 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.531A pdb=" N ALA B 13 " --> pdb=" O LYS B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.646A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.646A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.771A pdb=" N GLN B 150 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 198 " --> pdb=" O GLN B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.719A pdb=" N SER B 165 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 179 " --> pdb=" O SER B 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.771A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.847A pdb=" N ILE C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.140A pdb=" N TYR C 112 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 132 removed outlier: 4.789A pdb=" N LEU C 148 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 192 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 191 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS C 174 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 206 through 207 removed outlier: 4.241A pdb=" N CYS C 206 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 219 " --> pdb=" O CYS C 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.804A pdb=" N VAL D 12 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 37 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE D 115 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE D 35 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 20 through 22 Processing sheet with id=AB9, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.531A pdb=" N ALA E 13 " --> pdb=" O LYS E 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.646A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.646A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.772A pdb=" N GLN E 150 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 198 " --> pdb=" O GLN E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.718A pdb=" N SER E 165 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 179 " --> pdb=" O SER E 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.772A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.848A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 98 through 99 removed outlier: 4.140A pdb=" N TYR F 112 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 130 through 132 removed outlier: 4.789A pdb=" N LEU F 148 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL F 192 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL F 191 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS F 174 " --> pdb=" O VAL F 191 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 206 through 207 removed outlier: 4.242A pdb=" N CYS F 206 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS F 219 " --> pdb=" O CYS F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 226 hydrogen bonds defined for protein. 542 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: 1.11 Time building geometry restraints manager: 0.74 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: 1408 1.31 - 1.44: 2483 1.44 - 1.56: 4935 1.56 - 1.69: 4 1.69 - 1.81: 44 Bond restraints: 8874 Sorted by residual: bond pdb=" CA SER E 91 " pdb=" CB SER E 91 " ideal model delta sigma weight residual 1.527 1.439 0.088 1.30e-02 5.92e+03 4.61e+01 bond pdb=" CA SER B 91 " pdb=" CB SER B 91 " ideal model delta sigma weight residual 1.527 1.439 0.088 1.30e-02 5.92e+03 4.59e+01 bond pdb=" CA SER F 52 " pdb=" CB SER F 52 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.07e-02 8.73e+03 3.12e+01 bond pdb=" CA SER C 52 " pdb=" CB SER C 52 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.07e-02 8.73e+03 3.11e+01 bond pdb=" CA SER F 99 " pdb=" CB SER F 99 " ideal model delta sigma weight residual 1.530 1.450 0.080 1.62e-02 3.81e+03 2.43e+01 ... (remaining 8869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 11635 2.65 - 5.29: 395 5.29 - 7.94: 48 7.94 - 10.58: 6 10.58 - 13.23: 4 Bond angle restraints: 12088 Sorted by residual: angle pdb=" N LEU D 90 " pdb=" CA LEU D 90 " pdb=" C LEU D 90 " ideal model delta sigma weight residual 112.97 105.79 7.18 1.06e+00 8.90e-01 4.59e+01 angle pdb=" N LEU A 90 " pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 112.97 105.83 7.14 1.06e+00 8.90e-01 4.53e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 125.92 -12.02 1.80e+00 3.09e-01 4.46e+01 angle pdb=" CA TYR B 49 " pdb=" CB TYR B 49 " pdb=" CG TYR B 49 " ideal model delta sigma weight residual 113.90 125.90 -12.00 1.80e+00 3.09e-01 4.45e+01 angle pdb=" CA GLY B 96 " pdb=" C GLY B 96 " pdb=" O GLY B 96 " ideal model delta sigma weight residual 122.22 117.89 4.33 6.50e-01 2.37e+00 4.43e+01 ... (remaining 12083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4456 17.48 - 34.96: 604 34.96 - 52.43: 184 52.43 - 69.91: 42 69.91 - 87.39: 20 Dihedral angle restraints: 5306 sinusoidal: 2006 harmonic: 3300 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 138.36 41.64 0 5.00e+00 4.00e-02 6.94e+01 dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 138.38 41.62 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CB CYS E 137 " pdb=" SG CYS E 137 " pdb=" SG CYS E 197 " pdb=" CB CYS E 197 " ideal model delta sinusoidal sigma weight residual 93.00 23.63 69.37 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 5303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1093 0.064 - 0.128: 196 0.128 - 0.191: 44 0.191 - 0.255: 11 0.255 - 0.319: 6 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA ILE E 99 " pdb=" N ILE E 99 " pdb=" C ILE E 99 " pdb=" CB ILE E 99 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1347 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 98 " -0.776 9.50e-02 1.11e+02 3.48e-01 7.36e+01 pdb=" NE ARG C 98 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 98 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 98 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 98 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 98 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG F 98 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG F 98 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 98 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 98 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 39 " 0.071 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO E 40 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " 0.057 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 31 2.46 - 3.07: 5424 3.07 - 3.68: 12603 3.68 - 4.29: 18200 4.29 - 4.90: 31726 Nonbonded interactions: 67984 Sorted by model distance: nonbonded pdb=" O CYS E 217 " pdb=" NZ LYS F 228 " model vdw 1.852 3.120 nonbonded pdb=" OG SER D 65 " pdb=" O LYS D 67 " model vdw 2.191 3.040 nonbonded pdb=" OG SER A 65 " pdb=" O LYS A 67 " model vdw 2.191 3.040 nonbonded pdb=" NH1 ARG B 111 " pdb=" O ASP B 173 " model vdw 2.230 3.120 nonbonded pdb=" NH1 ARG E 111 " pdb=" O ASP E 173 " model vdw 2.230 3.120 ... (remaining 67979 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' 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=0.46 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: 3.310 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.007 0.093 8884 Z= 0.452 Angle : 1.095 13.231 12108 Z= 0.700 Chirality : 0.058 0.319 1350 Planarity : 0.016 0.348 1554 Dihedral : 18.397 87.388 3172 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 1.24 % Allowed : 7.17 % Favored : 91.59 % Rotamer: Outliers : 3.09 % Allowed : 30.56 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -4.20 (0.22), residues: 1136 helix: -1.99 (0.96), residues: 28 sheet: -2.67 (0.24), residues: 356 loop : -3.04 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 66 TYR 0.029 0.002 TYR E 49 PHE 0.016 0.001 PHE E 142 TRP 0.012 0.002 TRP C 102 HIS 0.003 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.45 ( 8874) covalent geometry : angle 1.09600 / 0.70 (12088) SS BOND : bond 0.00222 / 0.12 ( 10) SS BOND : angle 0.58996 / 0.36 ( 20) hydrogen bonds : bond 0.24685 / 17.19 ( 208) hydrogen bonds : angle 10.61129 / 7.37 ( 542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.352 Fit side-chains REVERT: A 91 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6962 (mm-40) REVERT: B 90 GLN cc_start: 0.8338 (tp40) cc_final: 0.8123 (tp40) REVERT: D 73 LEU cc_start: 0.8116 (mt) cc_final: 0.7822 (mt) REVERT: D 87 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: D 91 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6716 (mm-40) REVERT: E 21 ILE cc_start: 0.8159 (mp) cc_final: 0.7873 (mt) REVERT: F 63 SER cc_start: 0.7696 (p) cc_final: 0.7279 (t) REVERT: F 67 ARG cc_start: 0.7749 (ptt90) cc_final: 0.7518 (ptm-80) REVERT: F 80 TYR cc_start: 0.7648 (m-80) cc_final: 0.7360 (m-80) outliers start: 28 outliers final: 11 residues processed: 188 average time/residue: 0.0660 time to fit residues: 18.1502 Evaluate side-chains 166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 52 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 37 GLN B 89 GLN B 92 HIS B 163 GLN B 201 HIS C 107 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 201 HIS F 107 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148885 restraints weight = 27931.380| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 6.32 r_work: 0.3327 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8884 Z= 0.186 Angle : 0.695 10.340 12108 Z= 0.352 Chirality : 0.044 0.145 1350 Planarity : 0.008 0.077 1554 Dihedral : 7.125 76.111 1252 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.66 % Favored : 93.81 % Rotamer: Outliers : 3.81 % Allowed : 29.84 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.22), residues: 1136 helix: -1.45 (0.77), residues: 40 sheet: -2.04 (0.24), residues: 378 loop : -2.77 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.026 0.002 TYR B 49 PHE 0.015 0.002 PHE B 142 TRP 0.019 0.002 TRP D 125 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 8874) covalent geometry : angle 0.69484 / 0.35 (12088) SS BOND : bond 0.00248 / 0.14 ( 10) SS BOND : angle 0.58945 / 0.37 ( 20) hydrogen bonds : bond 0.03825 / 2.73 ( 208) hydrogen bonds : angle 6.53633 / 4.52 ( 542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.195 Fit side-chains REVERT: C 5 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8183 (t) REVERT: C 71 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8216 (t) REVERT: C 89 GLU cc_start: 0.8101 (pp20) cc_final: 0.7898 (pp20) REVERT: C 117 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8374 (p) REVERT: E 20 THR cc_start: 0.8518 (m) cc_final: 0.8280 (t) REVERT: E 63 SER cc_start: 0.7804 (t) cc_final: 0.7540 (p) REVERT: E 161 ASN cc_start: 0.3286 (t0) cc_final: 0.2688 (t0) REVERT: F 5 VAL cc_start: 0.8316 (m) cc_final: 0.8044 (t) REVERT: F 185 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5940 (pp) outliers start: 35 outliers final: 15 residues processed: 178 average time/residue: 0.0669 time to fit residues: 17.6291 Evaluate side-chains 163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 185 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150129 restraints weight = 29829.273| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 6.30 r_work: 0.3345 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8884 Z= 0.160 Angle : 0.642 9.086 12108 Z= 0.326 Chirality : 0.043 0.164 1350 Planarity : 0.007 0.075 1554 Dihedral : 6.306 69.471 1241 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.66 % Favored : 93.81 % Rotamer: Outliers : 4.73 % Allowed : 31.28 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.23), residues: 1136 helix: -1.33 (0.76), residues: 40 sheet: -1.49 (0.26), residues: 368 loop : -2.57 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 127 TYR 0.025 0.002 TYR B 49 PHE 0.019 0.001 PHE E 142 TRP 0.019 0.002 TRP D 125 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8874) covalent geometry : angle 0.64175 / 0.33 (12088) SS BOND : bond 0.00207 / 0.13 ( 10) SS BOND : angle 0.68061 / 0.38 ( 20) hydrogen bonds : bond 0.03459 / 2.48 ( 208) hydrogen bonds : angle 5.90988 / 4.07 ( 542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.371 Fit side-chains REVERT: A 9 LEU cc_start: 0.8459 (mt) cc_final: 0.8251 (mp) REVERT: B 12 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 45 LEU cc_start: 0.8539 (mt) cc_final: 0.8307 (mp) REVERT: D 100 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7989 (tp) REVERT: E 37 GLN cc_start: 0.8657 (tt0) cc_final: 0.8449 (tt0) REVERT: E 63 SER cc_start: 0.8045 (t) cc_final: 0.7836 (p) REVERT: F 5 VAL cc_start: 0.8442 (m) cc_final: 0.8215 (t) REVERT: F 7 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7665 (p) REVERT: F 185 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5933 (pp) outliers start: 44 outliers final: 27 residues processed: 174 average time/residue: 0.0659 time to fit residues: 17.2856 Evaluate side-chains 172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 102 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.190423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146970 restraints weight = 27994.857| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 6.15 r_work: 0.3321 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8884 Z= 0.213 Angle : 0.670 8.271 12108 Z= 0.342 Chirality : 0.045 0.178 1350 Planarity : 0.007 0.077 1554 Dihedral : 6.301 63.399 1238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.64 % Favored : 93.01 % Rotamer: Outliers : 4.94 % Allowed : 30.66 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.23), residues: 1136 helix: -1.30 (0.78), residues: 40 sheet: -1.10 (0.26), residues: 366 loop : -2.43 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 127 TYR 0.025 0.002 TYR B 49 PHE 0.018 0.002 PHE E 142 TRP 0.020 0.002 TRP D 125 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8874) covalent geometry : angle 0.66923 / 0.34 (12088) SS BOND : bond 0.00304 / 0.16 ( 10) SS BOND : angle 0.84318 / 0.46 ( 20) hydrogen bonds : bond 0.03409 / 2.46 ( 208) hydrogen bonds : angle 5.73123 / 3.95 ( 542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.313 Fit side-chains REVERT: A 72 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8302 (mtm180) REVERT: B 6 GLN cc_start: 0.7957 (tt0) cc_final: 0.7529 (tt0) REVERT: B 36 TYR cc_start: 0.8585 (m-80) cc_final: 0.8342 (m-80) REVERT: D 73 LEU cc_start: 0.8504 (mt) cc_final: 0.8285 (mp) REVERT: D 100 LEU cc_start: 0.8274 (tp) cc_final: 0.8047 (tp) outliers start: 46 outliers final: 33 residues processed: 187 average time/residue: 0.0700 time to fit residues: 19.8844 Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.0010 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.191525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141280 restraints weight = 43349.246| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 4.70 r_work: 0.3374 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8884 Z= 0.163 Angle : 0.627 7.581 12108 Z= 0.317 Chirality : 0.043 0.151 1350 Planarity : 0.007 0.073 1554 Dihedral : 6.027 57.102 1238 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.93 % Favored : 93.89 % Rotamer: Outliers : 5.35 % Allowed : 31.69 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.24), residues: 1136 helix: -1.10 (0.81), residues: 40 sheet: -0.81 (0.27), residues: 376 loop : -2.35 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 127 TYR 0.026 0.002 TYR E 49 PHE 0.015 0.001 PHE E 142 TRP 0.017 0.002 TRP A 125 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8874) covalent geometry : angle 0.62689 / 0.32 (12088) SS BOND : bond 0.00270 / 0.15 ( 10) SS BOND : angle 0.73324 / 0.42 ( 20) hydrogen bonds : bond 0.03184 / 2.29 ( 208) hydrogen bonds : angle 5.49467 / 3.77 ( 542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.268 Fit side-chains REVERT: B 12 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7814 (p) REVERT: C 215 THR cc_start: 0.4504 (OUTLIER) cc_final: 0.4198 (t) REVERT: D 59 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8079 (mtm) REVERT: D 73 LEU cc_start: 0.8454 (mt) cc_final: 0.8200 (mt) REVERT: E 49 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7764 (p90) REVERT: F 7 SER cc_start: 0.8181 (m) cc_final: 0.7909 (p) REVERT: F 215 THR cc_start: 0.4848 (OUTLIER) cc_final: 0.4601 (t) outliers start: 50 outliers final: 35 residues processed: 188 average time/residue: 0.0705 time to fit residues: 19.6715 Evaluate side-chains 186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 102 optimal weight: 30.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 GLN E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.189793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139250 restraints weight = 35965.347| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.55 r_work: 0.3335 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8884 Z= 0.246 Angle : 0.669 8.351 12108 Z= 0.343 Chirality : 0.044 0.144 1350 Planarity : 0.007 0.078 1554 Dihedral : 6.167 49.722 1238 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Rotamer: Outliers : 5.97 % Allowed : 31.28 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.24), residues: 1136 helix: -1.00 (0.81), residues: 40 sheet: -0.67 (0.26), residues: 406 loop : -2.34 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.025 0.002 TYR B 49 PHE 0.017 0.002 PHE C 68 TRP 0.020 0.002 TRP D 125 HIS 0.006 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 ( 8874) covalent geometry : angle 0.66869 / 0.34 (12088) SS BOND : bond 0.00283 / 0.16 ( 10) SS BOND : angle 0.86397 / 0.49 ( 20) hydrogen bonds : bond 0.03492 / 2.51 ( 208) hydrogen bonds : angle 5.62889 / 3.88 ( 542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 0.237 Fit side-chains REVERT: A 20 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 67 LYS cc_start: 0.8449 (pttp) cc_final: 0.8202 (pttp) REVERT: B 4 MET cc_start: 0.7931 (mmm) cc_final: 0.7500 (mtm) REVERT: B 6 GLN cc_start: 0.8020 (tt0) cc_final: 0.7623 (tt0) REVERT: B 18 ARG cc_start: 0.8653 (ptm-80) cc_final: 0.8360 (ptm160) REVERT: B 36 TYR cc_start: 0.8552 (m-80) cc_final: 0.8256 (m-80) REVERT: C 215 THR cc_start: 0.4470 (OUTLIER) cc_final: 0.4155 (t) REVERT: D 59 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8067 (mtm) REVERT: D 77 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8115 (p) REVERT: E 4 MET cc_start: 0.8000 (mmm) cc_final: 0.7485 (mtm) REVERT: E 10 SER cc_start: 0.7967 (p) cc_final: 0.7734 (p) REVERT: F 7 SER cc_start: 0.8329 (m) cc_final: 0.8102 (p) REVERT: F 25 SER cc_start: 0.8197 (m) cc_final: 0.7825 (p) REVERT: F 215 THR cc_start: 0.4915 (OUTLIER) cc_final: 0.4668 (t) outliers start: 56 outliers final: 37 residues processed: 185 average time/residue: 0.0643 time to fit residues: 17.8008 Evaluate side-chains 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.190575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140152 restraints weight = 34136.457| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 4.25 r_work: 0.3387 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8884 Z= 0.174 Angle : 0.628 7.520 12108 Z= 0.318 Chirality : 0.043 0.139 1350 Planarity : 0.007 0.073 1554 Dihedral : 6.020 48.028 1238 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.37 % Favored : 93.45 % Rotamer: Outliers : 4.84 % Allowed : 31.79 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.24), residues: 1136 helix: -0.89 (0.82), residues: 40 sheet: -0.37 (0.27), residues: 398 loop : -2.37 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.025 0.002 TYR B 49 PHE 0.018 0.002 PHE F 156 TRP 0.017 0.002 TRP D 125 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 8874) covalent geometry : angle 0.62791 / 0.32 (12088) SS BOND : bond 0.00258 / 0.15 ( 10) SS BOND : angle 0.79031 / 0.47 ( 20) hydrogen bonds : bond 0.03157 / 2.29 ( 208) hydrogen bonds : angle 5.42813 / 3.73 ( 542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.329 Fit side-chains REVERT: A 67 LYS cc_start: 0.8426 (pttp) cc_final: 0.8208 (pttp) REVERT: B 4 MET cc_start: 0.7904 (mmm) cc_final: 0.7581 (mtm) REVERT: B 18 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8308 (ptm160) REVERT: B 36 TYR cc_start: 0.8532 (m-80) cc_final: 0.8261 (m-80) REVERT: B 142 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5522 (p90) REVERT: C 215 THR cc_start: 0.4671 (OUTLIER) cc_final: 0.4351 (t) REVERT: D 77 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (p) REVERT: E 4 MET cc_start: 0.7986 (mmm) cc_final: 0.7545 (mtm) REVERT: F 7 SER cc_start: 0.8294 (m) cc_final: 0.8051 (p) REVERT: F 25 SER cc_start: 0.8155 (m) cc_final: 0.7780 (p) REVERT: F 215 THR cc_start: 0.5093 (OUTLIER) cc_final: 0.4833 (t) outliers start: 45 outliers final: 36 residues processed: 175 average time/residue: 0.0651 time to fit residues: 17.2383 Evaluate side-chains 180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN D 84 GLN E 89 GLN E 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.189696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139714 restraints weight = 34048.308| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.23 r_work: 0.3359 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8884 Z= 0.207 Angle : 0.649 7.683 12108 Z= 0.328 Chirality : 0.043 0.140 1350 Planarity : 0.007 0.075 1554 Dihedral : 6.031 45.730 1238 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.08 % Favored : 92.74 % Rotamer: Outliers : 5.56 % Allowed : 31.28 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.25), residues: 1136 helix: -0.75 (0.84), residues: 40 sheet: -0.42 (0.27), residues: 406 loop : -2.25 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.025 0.002 TYR E 49 PHE 0.017 0.002 PHE C 68 TRP 0.017 0.002 TRP D 125 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 8874) covalent geometry : angle 0.64817 / 0.33 (12088) SS BOND : bond 0.00246 / 0.14 ( 10) SS BOND : angle 0.85597 / 0.50 ( 20) hydrogen bonds : bond 0.03297 / 2.39 ( 208) hydrogen bonds : angle 5.50355 / 3.79 ( 542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.200 Fit side-chains REVERT: A 20 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 67 LYS cc_start: 0.8429 (pttp) cc_final: 0.8198 (pttp) REVERT: B 4 MET cc_start: 0.7898 (mmm) cc_final: 0.7601 (mtm) REVERT: B 18 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8317 (ptm160) REVERT: B 36 TYR cc_start: 0.8499 (m-80) cc_final: 0.8210 (m-80) REVERT: C 215 THR cc_start: 0.4786 (OUTLIER) cc_final: 0.4435 (t) REVERT: E 4 MET cc_start: 0.8019 (mmm) cc_final: 0.7604 (mtm) REVERT: E 22 THR cc_start: 0.8632 (m) cc_final: 0.8260 (p) REVERT: F 7 SER cc_start: 0.8300 (m) cc_final: 0.8079 (p) REVERT: F 25 SER cc_start: 0.8167 (m) cc_final: 0.7810 (p) REVERT: F 215 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.5079 (t) outliers start: 52 outliers final: 42 residues processed: 177 average time/residue: 0.0629 time to fit residues: 16.8512 Evaluate side-chains 184 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.190181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146065 restraints weight = 29853.027| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 6.18 r_work: 0.3288 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8884 Z= 0.202 Angle : 0.655 8.749 12108 Z= 0.329 Chirality : 0.043 0.140 1350 Planarity : 0.007 0.072 1554 Dihedral : 5.740 43.064 1235 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.46 % Favored : 93.36 % Rotamer: Outliers : 5.25 % Allowed : 31.28 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.25), residues: 1136 helix: -0.70 (0.84), residues: 40 sheet: -0.36 (0.27), residues: 406 loop : -2.24 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.024 0.002 TYR E 49 PHE 0.021 0.002 PHE B 142 TRP 0.017 0.002 TRP A 125 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 8874) covalent geometry : angle 0.65496 / 0.33 (12088) SS BOND : bond 0.00272 / 0.15 ( 10) SS BOND : angle 0.87780 / 0.52 ( 20) hydrogen bonds : bond 0.03308 / 2.38 ( 208) hydrogen bonds : angle 5.45657 / 3.75 ( 542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.293 Fit side-chains REVERT: A 20 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8271 (m) REVERT: A 67 LYS cc_start: 0.8521 (pttp) cc_final: 0.8236 (pttp) REVERT: A 77 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 4 MET cc_start: 0.8032 (mmm) cc_final: 0.7767 (mtm) REVERT: B 18 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8368 (ptm160) REVERT: B 36 TYR cc_start: 0.8580 (m-80) cc_final: 0.8319 (m-80) REVERT: C 215 THR cc_start: 0.4710 (OUTLIER) cc_final: 0.4414 (t) REVERT: D 77 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8160 (p) REVERT: E 4 MET cc_start: 0.8139 (mmm) cc_final: 0.7792 (mtm) REVERT: E 22 THR cc_start: 0.8708 (m) cc_final: 0.8349 (p) REVERT: F 7 SER cc_start: 0.8369 (m) cc_final: 0.8140 (p) REVERT: F 25 SER cc_start: 0.8250 (m) cc_final: 0.7877 (p) outliers start: 49 outliers final: 43 residues processed: 176 average time/residue: 0.0555 time to fit residues: 14.7213 Evaluate side-chains 186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 20 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145998 restraints weight = 29817.689| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 5.67 r_work: 0.3334 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8884 Z= 0.147 Angle : 0.626 9.041 12108 Z= 0.311 Chirality : 0.042 0.138 1350 Planarity : 0.006 0.071 1554 Dihedral : 5.543 43.706 1235 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.19 % Favored : 93.63 % Rotamer: Outliers : 4.42 % Allowed : 32.20 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.25), residues: 1136 helix: -0.74 (0.83), residues: 40 sheet: -0.28 (0.27), residues: 416 loop : -2.27 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.025 0.002 TYR E 49 PHE 0.020 0.001 PHE B 142 TRP 0.014 0.002 TRP A 125 HIS 0.004 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8874) covalent geometry : angle 0.62579 / 0.31 (12088) SS BOND : bond 0.00244 / 0.14 ( 10) SS BOND : angle 0.75811 / 0.44 ( 20) hydrogen bonds : bond 0.03126 / 2.27 ( 208) hydrogen bonds : angle 5.31159 / 3.63 ( 542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.318 Fit side-chains REVERT: A 20 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8187 (m) REVERT: A 67 LYS cc_start: 0.8468 (pttp) cc_final: 0.8186 (pttp) REVERT: A 77 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 18 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8324 (ptm160) REVERT: B 36 TYR cc_start: 0.8559 (m-80) cc_final: 0.8216 (m-80) REVERT: C 215 THR cc_start: 0.4707 (OUTLIER) cc_final: 0.4405 (t) REVERT: D 77 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (p) REVERT: E 4 MET cc_start: 0.8078 (mmm) cc_final: 0.7761 (mtm) REVERT: E 22 THR cc_start: 0.8642 (m) cc_final: 0.8282 (p) REVERT: E 49 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7679 (p90) REVERT: F 7 SER cc_start: 0.8301 (m) cc_final: 0.8050 (p) REVERT: F 25 SER cc_start: 0.8187 (m) cc_final: 0.7778 (p) outliers start: 41 outliers final: 34 residues processed: 169 average time/residue: 0.0588 time to fit residues: 15.2366 Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.192041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147712 restraints weight = 26769.418| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 5.52 r_work: 0.3363 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8884 Z= 0.148 Angle : 0.626 8.568 12108 Z= 0.311 Chirality : 0.042 0.138 1350 Planarity : 0.006 0.072 1554 Dihedral : 5.499 41.675 1235 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.19 % Favored : 93.63 % Rotamer: Outliers : 4.73 % Allowed : 31.89 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.25), residues: 1136 helix: -0.69 (0.84), residues: 40 sheet: -0.27 (0.28), residues: 400 loop : -2.19 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.025 0.002 TYR E 49 PHE 0.015 0.001 PHE B 142 TRP 0.014 0.002 TRP A 125 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8874) covalent geometry : angle 0.62596 / 0.31 (12088) SS BOND : bond 0.00234 / 0.13 ( 10) SS BOND : angle 0.81401 / 0.48 ( 20) hydrogen bonds : bond 0.03100 / 2.24 ( 208) hydrogen bonds : angle 5.26419 / 3.61 ( 542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2494.83 seconds wall clock time: 43 minutes 22.84 seconds (2602.84 seconds total)