Starting phenix.real_space_refine on Tue Jul 29 14:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.map" model { file = "/net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e27_30953/07_2025/7e27_30953.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 7575 2.51 5 N 1765 2.21 5 O 2040 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11475 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.50, per 1000 atoms: 0.48 Number of scatterers: 11475 At special positions: 0 Unit cell: (96.4678, 95.7932, 81.6266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 F 25 9.00 O 2040 8.00 N 1765 7.00 C 7575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 1 sheets defined 82.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR A 38 " --> pdb=" O LYS A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR B 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.957A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 273 through 291 removed outlier: 5.959A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR C 38 " --> pdb=" O LYS C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.454A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR D 38 " --> pdb=" O LYS D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 39 through 68 removed outlier: 3.841A pdb=" N PHE D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 181 through 206 removed outlier: 3.689A pdb=" N PHE D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.957A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 291 removed outlier: 5.959A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR E 38 " --> pdb=" O LYS E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.841A pdb=" N PHE E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 91 through 100 removed outlier: 4.327A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.454A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 164 through 177 Processing helix chain 'E' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 7.170A pdb=" N SER B 14 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE D 15 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS B 16 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL C 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER A 14 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 15 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS A 16 " --> pdb=" O ILE E 15 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.43: 3560 1.43 - 1.56: 6340 1.56 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11680 Sorted by residual: bond pdb=" C12 HV6 B 401 " pdb=" O21 HV6 B 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C12 HV6 A 401 " pdb=" O21 HV6 A 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 C 401 " pdb=" O21 HV6 C 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 D 401 " pdb=" O21 HV6 D 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C12 HV6 E 401 " pdb=" O21 HV6 E 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 11675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15210 2.06 - 4.12: 530 4.12 - 6.18: 75 6.18 - 8.25: 30 8.25 - 10.31: 5 Bond angle restraints: 15850 Sorted by residual: angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 109.81 120.12 -10.31 2.21e+00 2.05e-01 2.18e+01 angle pdb=" N PHE A 90 " pdb=" CA PHE A 90 " pdb=" C PHE A 90 " ideal model delta sigma weight residual 109.81 120.11 -10.30 2.21e+00 2.05e-01 2.17e+01 angle pdb=" N PHE B 90 " pdb=" CA PHE B 90 " pdb=" C PHE B 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE E 90 " pdb=" CA PHE E 90 " pdb=" C PHE E 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE C 90 " pdb=" CA PHE C 90 " pdb=" C PHE C 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 ... (remaining 15845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 5857 16.42 - 32.84: 608 32.84 - 49.27: 95 49.27 - 65.69: 40 65.69 - 82.11: 15 Dihedral angle restraints: 6615 sinusoidal: 2420 harmonic: 4195 Sorted by residual: dihedral pdb=" CA TYR E 70 " pdb=" C TYR E 70 " pdb=" N HIS E 71 " pdb=" CA HIS E 71 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR C 70 " pdb=" C TYR C 70 " pdb=" N HIS C 71 " pdb=" CA HIS C 71 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N HIS B 71 " pdb=" CA HIS B 71 " ideal model delta harmonic sigma weight residual 180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1508 0.068 - 0.137: 209 0.137 - 0.205: 38 0.205 - 0.273: 20 0.273 - 0.341: 15 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB VAL E 142 " pdb=" CA VAL E 142 " pdb=" CG1 VAL E 142 " pdb=" CG2 VAL E 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL C 142 " pdb=" CA VAL C 142 " pdb=" CG1 VAL C 142 " pdb=" CG2 VAL C 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB VAL A 142 " pdb=" CA VAL A 142 " pdb=" CG1 VAL A 142 " pdb=" CG2 VAL A 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1787 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR D 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR E 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 212 " -0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR B 212 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 212 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 212 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 212 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 212 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3927 2.84 - 3.35: 10752 3.35 - 3.87: 21475 3.87 - 4.38: 25395 4.38 - 4.90: 42009 Nonbonded interactions: 103558 Sorted by model distance: nonbonded pdb=" O ALA E 226 " pdb=" O HOH E 501 " model vdw 2.322 3.040 nonbonded pdb=" N ASP E 208 " pdb=" OD1 ASP E 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP B 208 " pdb=" OD1 ASP B 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP A 208 " pdb=" OD1 ASP A 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP D 208 " pdb=" OD1 ASP D 208 " model vdw 2.332 3.120 ... (remaining 103553 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.680 Find NCS groups from input model: 0.220 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:15.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 0.094 11680 Z= 0.341 Angle : 0.911 10.307 15850 Z= 0.513 Chirality : 0.061 0.341 1790 Planarity : 0.006 0.033 1930 Dihedral : 14.587 82.111 3965 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.42 % Allowed : 5.08 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 1425 helix: -1.34 (0.12), residues: 1145 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 59 PHE 0.042 0.004 PHE C 223 TYR 0.050 0.003 TYR B 212 ARG 0.001 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.12179 ( 841) hydrogen bonds : angle 6.18439 ( 2517) covalent geometry : bond 0.00739 (11680) covalent geometry : angle 0.91057 (15850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 1.174 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 169 average time/residue: 1.4278 time to fit residues: 259.3641 Evaluate side-chains 133 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain E residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 265 ASN B 71 HIS B 265 ASN C 71 HIS C 265 ASN D 71 HIS D 265 ASN E 71 HIS E 265 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.088784 restraints weight = 12370.451| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.21 r_work: 0.2875 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11680 Z= 0.136 Angle : 0.548 7.215 15850 Z= 0.306 Chirality : 0.041 0.143 1790 Planarity : 0.004 0.027 1930 Dihedral : 4.909 33.339 1599 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.12 % Allowed : 9.49 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1425 helix: 0.70 (0.14), residues: 1130 sheet: None (None), residues: 0 loop : -1.60 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 165 PHE 0.024 0.002 PHE B 223 TYR 0.018 0.002 TYR A 236 ARG 0.001 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 841) hydrogen bonds : angle 4.46555 ( 2517) covalent geometry : bond 0.00285 (11680) covalent geometry : angle 0.54805 (15850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.238 Fit side-chains REVERT: A 201 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 283 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6563 (pm20) REVERT: B 201 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 283 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6456 (pm20) REVERT: C 283 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6553 (pm20) REVERT: D 201 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: E 201 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: E 283 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6677 (pm20) outliers start: 25 outliers final: 10 residues processed: 161 average time/residue: 1.2932 time to fit residues: 224.5614 Evaluate side-chains 148 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS B 265 ASN D 179 HIS E 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.084634 restraints weight = 12492.391| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.21 r_work: 0.2810 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11680 Z= 0.179 Angle : 0.606 7.446 15850 Z= 0.338 Chirality : 0.045 0.160 1790 Planarity : 0.004 0.026 1930 Dihedral : 4.908 25.333 1595 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.39 % Allowed : 9.24 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1425 helix: 1.20 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.72 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 165 PHE 0.026 0.002 PHE D 223 TYR 0.019 0.002 TYR A 236 ARG 0.001 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.05791 ( 841) hydrogen bonds : angle 4.50526 ( 2517) covalent geometry : bond 0.00403 (11680) covalent geometry : angle 0.60613 (15850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.306 Fit side-chains REVERT: A 201 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: A 283 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6451 (pm20) REVERT: B 201 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 283 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6491 (pm20) REVERT: C 283 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6566 (pm20) REVERT: D 201 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: D 223 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7222 (p90) REVERT: D 247 LYS cc_start: 0.8261 (mttt) cc_final: 0.8055 (ttmm) REVERT: E 201 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8051 (m-80) outliers start: 40 outliers final: 19 residues processed: 167 average time/residue: 1.2524 time to fit residues: 226.2869 Evaluate side-chains 163 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 0.0070 chunk 71 optimal weight: 8.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.088114 restraints weight = 12426.195| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.22 r_work: 0.2864 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11680 Z= 0.125 Angle : 0.527 7.129 15850 Z= 0.293 Chirality : 0.040 0.154 1790 Planarity : 0.003 0.024 1930 Dihedral : 4.589 27.040 1595 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.71 % Allowed : 11.19 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1425 helix: 1.63 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 59 PHE 0.022 0.002 PHE D 223 TYR 0.014 0.001 TYR A 236 ARG 0.001 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 841) hydrogen bonds : angle 4.26804 ( 2517) covalent geometry : bond 0.00252 (11680) covalent geometry : angle 0.52699 (15850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.535 Fit side-chains REVERT: A 201 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: A 283 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6523 (pm20) REVERT: B 201 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: B 283 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6469 (pm20) REVERT: C 283 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6514 (pm20) REVERT: D 201 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: E 283 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6578 (pm20) outliers start: 32 outliers final: 16 residues processed: 163 average time/residue: 1.6709 time to fit residues: 292.6835 Evaluate side-chains 150 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 179 HIS D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.083020 restraints weight = 12393.428| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.20 r_work: 0.2784 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11680 Z= 0.216 Angle : 0.644 7.456 15850 Z= 0.359 Chirality : 0.048 0.199 1790 Planarity : 0.004 0.026 1930 Dihedral : 4.970 26.999 1595 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.80 % Allowed : 11.53 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1425 helix: 1.40 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.64 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 284 PHE 0.028 0.003 PHE D 223 TYR 0.019 0.002 TYR A 236 ARG 0.002 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.06196 ( 841) hydrogen bonds : angle 4.56126 ( 2517) covalent geometry : bond 0.00503 (11680) covalent geometry : angle 0.64363 (15850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.304 Fit side-chains REVERT: A 201 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: B 201 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: B 283 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6481 (pm20) REVERT: C 283 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6483 (pm20) REVERT: D 201 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: E 201 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7994 (m-80) outliers start: 33 outliers final: 16 residues processed: 165 average time/residue: 1.4564 time to fit residues: 259.2904 Evaluate side-chains 157 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN D 265 ASN E 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.088987 restraints weight = 12547.063| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.22 r_work: 0.2877 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11680 Z= 0.118 Angle : 0.512 6.937 15850 Z= 0.284 Chirality : 0.039 0.154 1790 Planarity : 0.003 0.024 1930 Dihedral : 4.493 27.329 1595 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.78 % Allowed : 12.80 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1425 helix: 1.80 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 59 PHE 0.021 0.002 PHE A 223 TYR 0.015 0.001 TYR C 286 ARG 0.001 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 841) hydrogen bonds : angle 4.21523 ( 2517) covalent geometry : bond 0.00232 (11680) covalent geometry : angle 0.51216 (15850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.563 Fit side-chains REVERT: A 201 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: B 201 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 283 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6480 (pm20) REVERT: C 283 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6466 (pm20) REVERT: D 201 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: E 283 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6494 (pm20) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 1.7213 time to fit residues: 286.6394 Evaluate side-chains 147 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN D 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.083602 restraints weight = 12658.600| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.22 r_work: 0.2793 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11680 Z= 0.198 Angle : 0.623 7.376 15850 Z= 0.347 Chirality : 0.047 0.182 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.879 26.471 1595 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.54 % Allowed : 12.12 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1425 helix: 1.53 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.59 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 284 PHE 0.026 0.002 PHE D 223 TYR 0.018 0.002 TYR A 286 ARG 0.002 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 841) hydrogen bonds : angle 4.49397 ( 2517) covalent geometry : bond 0.00454 (11680) covalent geometry : angle 0.62303 (15850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.598 Fit side-chains REVERT: A 201 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 201 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: B 283 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6493 (pm20) REVERT: C 283 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6479 (pm20) REVERT: D 201 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: E 201 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7969 (m-80) outliers start: 30 outliers final: 17 residues processed: 154 average time/residue: 1.7846 time to fit residues: 297.6823 Evaluate side-chains 156 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN D 265 ASN E 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.088771 restraints weight = 12444.302| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.21 r_work: 0.2855 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11680 Z= 0.119 Angle : 0.515 6.974 15850 Z= 0.285 Chirality : 0.039 0.155 1790 Planarity : 0.003 0.024 1930 Dihedral : 4.491 27.567 1595 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.12 % Allowed : 12.97 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1425 helix: 1.85 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.59 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 59 PHE 0.021 0.002 PHE A 223 TYR 0.019 0.001 TYR A 286 ARG 0.001 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 841) hydrogen bonds : angle 4.21377 ( 2517) covalent geometry : bond 0.00236 (11680) covalent geometry : angle 0.51464 (15850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.246 Fit side-chains REVERT: A 201 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: B 201 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 283 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6502 (pm20) REVERT: C 283 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6429 (pm20) REVERT: D 201 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: E 283 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6502 (pm20) outliers start: 25 outliers final: 19 residues processed: 155 average time/residue: 1.2210 time to fit residues: 205.3111 Evaluate side-chains 151 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 265 ASN D 265 ASN E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.093784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.081834 restraints weight = 12690.247| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.21 r_work: 0.2765 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11680 Z= 0.267 Angle : 0.697 8.027 15850 Z= 0.388 Chirality : 0.053 0.246 1790 Planarity : 0.004 0.026 1930 Dihedral : 5.102 28.884 1595 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.54 % Allowed : 12.46 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1425 helix: 1.37 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.52 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 284 PHE 0.029 0.003 PHE D 223 TYR 0.021 0.003 TYR D 221 ARG 0.003 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.06687 ( 841) hydrogen bonds : angle 4.64691 ( 2517) covalent geometry : bond 0.00636 (11680) covalent geometry : angle 0.69654 (15850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.164 Fit side-chains REVERT: A 201 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 223 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7852 (p90) REVERT: B 201 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 283 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6508 (pm20) REVERT: C 283 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6501 (pm20) REVERT: D 201 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: E 201 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8034 (m-80) outliers start: 30 outliers final: 16 residues processed: 161 average time/residue: 1.4341 time to fit residues: 250.1369 Evaluate side-chains 154 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 284 HIS B 265 ASN C 265 ASN D 265 ASN E 284 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.087832 restraints weight = 12481.170| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.22 r_work: 0.2859 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11680 Z= 0.126 Angle : 0.531 7.247 15850 Z= 0.294 Chirality : 0.040 0.156 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.609 28.835 1595 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.78 % Allowed : 13.47 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1425 helix: 1.76 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.58 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 59 PHE 0.022 0.002 PHE B 223 TYR 0.014 0.001 TYR D 236 ARG 0.001 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 841) hydrogen bonds : angle 4.26682 ( 2517) covalent geometry : bond 0.00253 (11680) covalent geometry : angle 0.53061 (15850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.223 Fit side-chains REVERT: A 201 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 201 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: B 283 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6483 (pm20) REVERT: C 283 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6458 (pm20) REVERT: D 201 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: E 283 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6482 (pm20) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 1.3358 time to fit residues: 218.7139 Evaluate side-chains 154 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 118 optimal weight: 0.0000 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.087523 restraints weight = 12407.909| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.21 r_work: 0.2854 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11680 Z= 0.130 Angle : 0.537 7.097 15850 Z= 0.298 Chirality : 0.040 0.156 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.537 26.221 1595 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 13.73 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.22), residues: 1425 helix: 1.82 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.57 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 59 PHE 0.022 0.002 PHE B 223 TYR 0.013 0.001 TYR D 236 ARG 0.001 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 841) hydrogen bonds : angle 4.25076 ( 2517) covalent geometry : bond 0.00266 (11680) covalent geometry : angle 0.53748 (15850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8578.85 seconds wall clock time: 155 minutes 54.57 seconds (9354.57 seconds total)