Starting phenix.real_space_refine on Tue Mar 3 19:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2026/6jxr_9895.map" } resolution = 3.7 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5379 2.51 5 N 1386 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8437 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 260 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "d" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "f" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 904 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 111} Chain: "m" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 235} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Time building chain proxies: 1.80, per 1000 atoms: 0.21 Number of scatterers: 8437 At special positions: 0 Unit cell: (116.27, 90.902, 133.182, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1618 8.00 N 1386 7.00 C 5379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.02 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.02 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.03 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.03 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.03 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.02 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " 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: 0.61 Conformation dependent library (CDL) restraints added in 380.6 milliseconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 26.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'a' and resid 28 through 57 removed outlier: 4.572A pdb=" N CYS a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 54 removed outlier: 4.132A pdb=" N LEU b 31 " --> pdb=" O LEU b 27 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR b 42 " --> pdb=" O ILE b 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 128 removed outlier: 3.763A pdb=" N HIS d 128 " --> pdb=" O CYS d 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 Processing helix chain 'f' and resid 128 through 155 Processing helix chain 'g' and resid 111 through 137 Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.518A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 106' Processing helix chain 'm' and resid 204 through 208 removed outlier: 3.570A pdb=" N ALA m 208 " --> pdb=" O CYS m 205 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 233 removed outlier: 3.731A pdb=" N VAL m 232 " --> pdb=" O ASP m 228 " (cutoff:3.500A) Processing helix chain 'm' and resid 239 through 273 removed outlier: 3.633A pdb=" N ASN m 243 " --> pdb=" O ASP m 239 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 4.263A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.639A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 269 through 308 Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 3.529A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 5.516A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.849A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N TYR e 111 " --> pdb=" O GLU d 83 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'f' and resid 65 through 66 removed outlier: 4.110A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123 removed outlier: 3.756A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.575A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 27 through 28 Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.196A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER m 114 " --> pdb=" O TYR m 54 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP m 57 " --> pdb=" O LEU m 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.196A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 140 through 143 removed outlier: 3.947A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA m 196 " --> pdb=" O CYS m 155 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET m 184 " --> pdb=" O PHE m 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'n' and resid 23 through 26 Processing sheet with id=AB4, first strand: chain 'n' and resid 29 through 33 removed outlier: 3.509A pdb=" N LEU n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR n 133 " --> pdb=" O LEU n 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.244A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 183 through 184 removed outlier: 3.746A pdb=" N ALA n 256 " --> pdb=" O CYS n 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 37 through 41 401 hydrogen bonds defined for protein. 1083 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: 1.18 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2693 1.34 - 1.46: 2032 1.46 - 1.59: 3817 1.59 - 1.71: 1 1.71 - 1.83: 76 Bond restraints: 8619 Sorted by residual: bond pdb=" CE LYS m 190 " pdb=" NZ LYS m 190 " ideal model delta sigma weight residual 1.489 1.620 -0.131 3.00e-02 1.11e+03 1.90e+01 bond pdb=" CB VAL d 33 " pdb=" CG2 VAL d 33 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.78e+00 bond pdb=" C PHE n 147 " pdb=" N GLU n 148 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" CB VAL m 154 " pdb=" CG2 VAL m 154 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CG ARG d 57 " pdb=" CD ARG d 57 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 ... (remaining 8614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 11382 2.59 - 5.18: 257 5.18 - 7.76: 35 7.76 - 10.35: 9 10.35 - 12.94: 4 Bond angle restraints: 11687 Sorted by residual: angle pdb=" C THR m 158 " pdb=" N ASP m 159 " pdb=" CA ASP m 159 " ideal model delta sigma weight residual 121.54 134.48 -12.94 1.91e+00 2.74e-01 4.59e+01 angle pdb=" C LEU b 27 " pdb=" N ASP b 28 " pdb=" CA ASP b 28 " ideal model delta sigma weight residual 121.62 130.41 -8.79 1.57e+00 4.06e-01 3.13e+01 angle pdb=" N PHE n 219 " pdb=" CA PHE n 219 " pdb=" C PHE n 219 " ideal model delta sigma weight residual 114.04 107.14 6.90 1.24e+00 6.50e-01 3.10e+01 angle pdb=" C THR d 76 " pdb=" N ASP d 77 " pdb=" CA ASP d 77 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PHE m 160 " pdb=" CA PHE m 160 " pdb=" C PHE m 160 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 ... (remaining 11682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 4882 15.70 - 31.40: 204 31.40 - 47.10: 65 47.10 - 62.80: 15 62.80 - 78.50: 10 Dihedral angle restraints: 5176 sinusoidal: 2056 harmonic: 3120 Sorted by residual: dihedral pdb=" CA ASP m 217 " pdb=" C ASP m 217 " pdb=" N THR m 218 " pdb=" CA THR m 218 " ideal model delta harmonic sigma weight residual 180.00 129.80 50.20 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ILE b 38 " pdb=" C ILE b 38 " pdb=" N LEU b 39 " pdb=" CA LEU b 39 " ideal model delta harmonic sigma weight residual 180.00 132.28 47.72 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ASP m 159 " pdb=" C ASP m 159 " pdb=" N PHE m 160 " pdb=" CA PHE m 160 " ideal model delta harmonic sigma weight residual 180.00 144.29 35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1040 0.068 - 0.135: 241 0.135 - 0.203: 22 0.203 - 0.270: 5 0.270 - 0.338: 1 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CB ILE d 78 " pdb=" CA ILE d 78 " pdb=" CG1 ILE d 78 " pdb=" CG2 ILE d 78 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR d 79 " pdb=" N TYR d 79 " pdb=" C TYR d 79 " pdb=" CB TYR d 79 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1306 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE m 157 " -0.022 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE m 157 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE m 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE m 157 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE m 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE m 157 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE m 157 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO n 223 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE n 140 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO n 141 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO n 141 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO n 141 " 0.036 5.00e-02 4.00e+02 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2100 2.80 - 3.32: 7266 3.32 - 3.85: 13211 3.85 - 4.37: 14744 4.37 - 4.90: 26395 Nonbonded interactions: 63716 Sorted by model distance: nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.273 3.040 nonbonded pdb=" O THR d 47 " pdb=" OH TYR d 71 " model vdw 2.289 3.040 nonbonded pdb=" NH1 ARG d 57 " pdb=" O ARG m 185 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASP g 35 " pdb=" OH TYR g 101 " model vdw 2.303 3.040 nonbonded pdb=" O PHE m 160 " pdb=" OG1 THR m 164 " model vdw 2.313 3.040 ... (remaining 63711 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 24 through 55) selection = chain 'b' } ncs_group { reference = chain 'e' selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.080 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.008 0.131 8633 Z= 0.329 Angle : 1.015 12.938 11715 Z= 0.560 Chirality : 0.057 0.338 1309 Planarity : 0.007 0.076 1492 Dihedral : 10.827 78.503 3132 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 0.74 % Allowed : 3.72 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.45 (0.21), residues: 1057 helix: -1.00 (0.26), residues: 249 sheet: -1.78 (0.27), residues: 270 loop : -3.29 (0.21), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG n 228 TYR 0.039 0.003 TYR e 149 PHE 0.058 0.003 PHE m 157 TRP 0.023 0.003 TRP n 179 HIS 0.008 0.002 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 8619) covalent geometry : angle 1.01077 (11687) SS BOND : bond 0.00522 ( 14) SS BOND : angle 2.05565 ( 28) hydrogen bonds : bond 0.12255 ( 397) hydrogen bonds : angle 6.13083 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 350 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 111 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: m 138 ASP cc_start: 0.7993 (t0) cc_final: 0.7781 (t0) REVERT: n 69 VAL cc_start: 0.8985 (m) cc_final: 0.8726 (p) REVERT: n 208 CYS cc_start: 0.8035 (m) cc_final: 0.7004 (m) outliers start: 7 outliers final: 3 residues processed: 356 average time/residue: 0.0846 time to fit residues: 41.7283 Evaluate side-chains 211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 94 GLN f 92 GLN g 28 ASN m 28 GLN m 199 ASN m 211 ASN n 122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110604 restraints weight = 13328.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114953 restraints weight = 8163.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116442 restraints weight = 5444.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116473 restraints weight = 4564.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116832 restraints weight = 4650.843| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8633 Z= 0.138 Angle : 0.704 11.715 11715 Z= 0.365 Chirality : 0.045 0.276 1309 Planarity : 0.005 0.047 1492 Dihedral : 6.790 59.643 1167 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 2.98 % Allowed : 14.03 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.08 (0.24), residues: 1057 helix: 1.07 (0.30), residues: 263 sheet: -1.17 (0.28), residues: 285 loop : -2.95 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 185 TYR 0.026 0.002 TYR n 50 PHE 0.021 0.001 PHE m 157 TRP 0.013 0.001 TRP m 271 HIS 0.002 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8619) covalent geometry : angle 0.69997 (11687) SS BOND : bond 0.00573 ( 14) SS BOND : angle 1.67896 ( 28) hydrogen bonds : bond 0.03827 ( 397) hydrogen bonds : angle 4.92733 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.8751 (tp) cc_final: 0.8457 (mt) REVERT: a 50 PHE cc_start: 0.7129 (t80) cc_final: 0.6527 (t80) REVERT: d 91 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8452 (ttp80) REVERT: f 75 ILE cc_start: 0.8808 (mt) cc_final: 0.8561 (mp) REVERT: f 86 GLU cc_start: 0.8345 (mp0) cc_final: 0.7947 (mp0) REVERT: f 111 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: f 122 CYS cc_start: 0.3807 (t) cc_final: 0.3257 (t) REVERT: f 128 MET cc_start: 0.6731 (ppp) cc_final: 0.6185 (ppp) REVERT: g 109 GLU cc_start: 0.7427 (mp0) cc_final: 0.7175 (mm-30) REVERT: m 63 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7355 (mmm160) REVERT: m 207 ASN cc_start: 0.8069 (t0) cc_final: 0.7688 (t0) REVERT: m 233 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7148 (mm-30) REVERT: n 38 MET cc_start: 0.8483 (tpp) cc_final: 0.7843 (tmm) REVERT: n 204 ASP cc_start: 0.7997 (p0) cc_final: 0.7728 (p0) REVERT: e 64 LYS cc_start: 0.8378 (tptm) cc_final: 0.7910 (mtmt) outliers start: 28 outliers final: 22 residues processed: 254 average time/residue: 0.0870 time to fit residues: 30.6207 Evaluate side-chains 228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 75 ASP Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 190 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 122 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 211 ASN n 104 GLN n 221 GLN e 61 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109896 restraints weight = 13103.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113300 restraints weight = 8522.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114516 restraints weight = 5804.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114959 restraints weight = 5325.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115518 restraints weight = 4964.697| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8633 Z= 0.141 Angle : 0.655 9.861 11715 Z= 0.341 Chirality : 0.044 0.254 1309 Planarity : 0.004 0.051 1492 Dihedral : 6.628 59.970 1167 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.36 % Allowed : 14.67 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1057 helix: 2.04 (0.31), residues: 261 sheet: -0.53 (0.30), residues: 273 loop : -2.71 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 269 TYR 0.023 0.002 TYR n 50 PHE 0.020 0.001 PHE m 157 TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8619) covalent geometry : angle 0.64783 (11687) SS BOND : bond 0.00394 ( 14) SS BOND : angle 2.03742 ( 28) hydrogen bonds : bond 0.03680 ( 397) hydrogen bonds : angle 4.58830 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7252 (t80) cc_final: 0.6752 (t80) REVERT: d 55 ILE cc_start: 0.8161 (tt) cc_final: 0.7923 (tt) REVERT: f 86 GLU cc_start: 0.8328 (mp0) cc_final: 0.7910 (mp0) REVERT: f 111 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: f 123 MET cc_start: 0.5847 (mtt) cc_final: 0.5618 (mtt) REVERT: g 25 ILE cc_start: 0.8780 (mm) cc_final: 0.8372 (mm) REVERT: g 109 GLU cc_start: 0.7487 (mp0) cc_final: 0.6930 (mp0) REVERT: m 63 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7353 (mmm160) REVERT: m 207 ASN cc_start: 0.8142 (t0) cc_final: 0.7843 (t0) REVERT: n 32 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8119 (pp) REVERT: n 38 MET cc_start: 0.8423 (tpp) cc_final: 0.7995 (tmm) REVERT: n 73 ILE cc_start: 0.8582 (mp) cc_final: 0.7947 (tp) REVERT: n 204 ASP cc_start: 0.8202 (p0) cc_final: 0.7820 (p0) REVERT: e 64 LYS cc_start: 0.8437 (tptm) cc_final: 0.7986 (mtmt) outliers start: 41 outliers final: 28 residues processed: 248 average time/residue: 0.0816 time to fit residues: 28.2946 Evaluate side-chains 230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 268 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 103 SER Chi-restraints excluded: chain e residue 122 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 72 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 0.0000 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106871 restraints weight = 13502.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110679 restraints weight = 7906.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113190 restraints weight = 5611.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114756 restraints weight = 4529.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115878 restraints weight = 3952.578| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8633 Z= 0.117 Angle : 0.621 9.583 11715 Z= 0.321 Chirality : 0.043 0.202 1309 Planarity : 0.004 0.050 1492 Dihedral : 6.253 57.909 1167 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.93 % Allowed : 16.26 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1057 helix: 2.48 (0.31), residues: 263 sheet: -0.23 (0.30), residues: 274 loop : -2.51 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 269 TYR 0.018 0.001 TYR n 50 PHE 0.019 0.001 PHE m 157 TRP 0.009 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8619) covalent geometry : angle 0.61523 (11687) SS BOND : bond 0.00284 ( 14) SS BOND : angle 1.84010 ( 28) hydrogen bonds : bond 0.03417 ( 397) hydrogen bonds : angle 4.31360 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7245 (t80) cc_final: 0.6744 (t80) REVERT: b 40 PHE cc_start: 0.7973 (t80) cc_final: 0.7644 (t80) REVERT: f 86 GLU cc_start: 0.8361 (mp0) cc_final: 0.7921 (mp0) REVERT: f 89 GLU cc_start: 0.8002 (tt0) cc_final: 0.7749 (tt0) REVERT: f 90 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8122 (mm) REVERT: f 111 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: f 150 TYR cc_start: 0.7474 (m-80) cc_final: 0.7149 (t80) REVERT: m 269 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6524 (ttp80) REVERT: n 32 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8118 (pp) REVERT: n 73 ILE cc_start: 0.8586 (mp) cc_final: 0.8025 (tp) REVERT: n 204 ASP cc_start: 0.8223 (p0) cc_final: 0.7787 (p0) REVERT: e 64 LYS cc_start: 0.8430 (tptm) cc_final: 0.7932 (mtmt) outliers start: 37 outliers final: 24 residues processed: 244 average time/residue: 0.0841 time to fit residues: 28.7629 Evaluate side-chains 232 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 103 SER Chi-restraints excluded: chain e residue 122 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 0.8980 chunk 95 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 28 GLN m 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107273 restraints weight = 13408.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111353 restraints weight = 8226.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112615 restraints weight = 5513.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112774 restraints weight = 4748.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113045 restraints weight = 4781.178| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8633 Z= 0.131 Angle : 0.623 9.247 11715 Z= 0.324 Chirality : 0.043 0.204 1309 Planarity : 0.004 0.042 1492 Dihedral : 5.857 56.537 1165 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.14 % Allowed : 17.64 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 1057 helix: 2.79 (0.31), residues: 261 sheet: 0.02 (0.32), residues: 261 loop : -2.31 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 91 TYR 0.016 0.001 TYR n 271 PHE 0.016 0.001 PHE m 157 TRP 0.010 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8619) covalent geometry : angle 0.61885 (11687) SS BOND : bond 0.00311 ( 14) SS BOND : angle 1.62596 ( 28) hydrogen bonds : bond 0.03401 ( 397) hydrogen bonds : angle 4.24243 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7322 (t80) cc_final: 0.7111 (t80) REVERT: b 40 PHE cc_start: 0.7982 (t80) cc_final: 0.7664 (t80) REVERT: f 86 GLU cc_start: 0.8371 (mp0) cc_final: 0.7903 (mp0) REVERT: f 90 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (mm) REVERT: f 111 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: f 150 TYR cc_start: 0.7536 (m-80) cc_final: 0.7169 (t80) REVERT: g 38 GLU cc_start: 0.6929 (pm20) cc_final: 0.6104 (mp0) REVERT: m 126 THR cc_start: 0.9193 (m) cc_final: 0.8931 (p) REVERT: m 269 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6614 (ttp80) REVERT: n 32 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8124 (pp) REVERT: n 73 ILE cc_start: 0.8630 (mp) cc_final: 0.8102 (tp) REVERT: n 204 ASP cc_start: 0.8243 (p0) cc_final: 0.7821 (p0) REVERT: e 64 LYS cc_start: 0.8438 (tptm) cc_final: 0.7920 (mtmt) REVERT: e 101 ARG cc_start: 0.7540 (mmm160) cc_final: 0.6989 (mmt180) outliers start: 39 outliers final: 29 residues processed: 231 average time/residue: 0.0854 time to fit residues: 27.3943 Evaluate side-chains 225 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102069 restraints weight = 13510.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103636 restraints weight = 9881.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105069 restraints weight = 7388.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106190 restraints weight = 6072.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106539 restraints weight = 5562.028| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8633 Z= 0.236 Angle : 0.705 9.657 11715 Z= 0.369 Chirality : 0.045 0.212 1309 Planarity : 0.004 0.041 1492 Dihedral : 6.082 57.761 1165 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.99 % Allowed : 18.49 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.26), residues: 1057 helix: 2.75 (0.31), residues: 256 sheet: -0.00 (0.31), residues: 268 loop : -2.35 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 91 TYR 0.014 0.002 TYR m 54 PHE 0.024 0.002 PHE m 262 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 8619) covalent geometry : angle 0.69609 (11687) SS BOND : bond 0.00406 ( 14) SS BOND : angle 2.34412 ( 28) hydrogen bonds : bond 0.03906 ( 397) hydrogen bonds : angle 4.47699 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7329 (t80) cc_final: 0.7049 (t80) REVERT: b 40 PHE cc_start: 0.8080 (t80) cc_final: 0.7807 (t80) REVERT: f 86 GLU cc_start: 0.8420 (mp0) cc_final: 0.7997 (mp0) REVERT: f 88 SER cc_start: 0.8671 (t) cc_final: 0.8319 (p) REVERT: f 90 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8394 (mm) REVERT: f 111 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: n 32 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8050 (pp) REVERT: n 73 ILE cc_start: 0.8676 (mp) cc_final: 0.8058 (tp) REVERT: n 204 ASP cc_start: 0.8363 (p0) cc_final: 0.7934 (p0) REVERT: e 58 LEU cc_start: 0.8953 (mm) cc_final: 0.8623 (mm) REVERT: e 64 LYS cc_start: 0.8547 (tptm) cc_final: 0.7952 (mtmt) REVERT: e 78 ASP cc_start: 0.7204 (t70) cc_final: 0.6927 (t0) REVERT: e 92 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: e 101 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7211 (mtt180) outliers start: 47 outliers final: 35 residues processed: 227 average time/residue: 0.0828 time to fit residues: 26.5114 Evaluate side-chains 223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102014 restraints weight = 13682.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104214 restraints weight = 9910.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105613 restraints weight = 7242.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106410 restraints weight = 5803.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106719 restraints weight = 5408.673| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8633 Z= 0.219 Angle : 0.694 9.395 11715 Z= 0.364 Chirality : 0.045 0.223 1309 Planarity : 0.004 0.043 1492 Dihedral : 6.026 52.114 1165 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 5.31 % Allowed : 19.13 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1057 helix: 2.74 (0.31), residues: 256 sheet: -0.08 (0.32), residues: 266 loop : -2.35 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 91 TYR 0.016 0.002 TYR d 71 PHE 0.023 0.002 PHE m 157 TRP 0.011 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8619) covalent geometry : angle 0.68762 (11687) SS BOND : bond 0.00381 ( 14) SS BOND : angle 2.00783 ( 28) hydrogen bonds : bond 0.03857 ( 397) hydrogen bonds : angle 4.48691 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: f 86 GLU cc_start: 0.8429 (mp0) cc_final: 0.7999 (mp0) REVERT: f 88 SER cc_start: 0.8745 (t) cc_final: 0.8382 (p) REVERT: f 90 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8362 (mm) REVERT: f 101 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8262 (ttp-110) REVERT: f 111 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: f 128 MET cc_start: 0.6848 (ppp) cc_final: 0.6569 (ppp) REVERT: g 38 GLU cc_start: 0.7029 (pm20) cc_final: 0.6222 (mp0) REVERT: g 84 MET cc_start: 0.8249 (mmp) cc_final: 0.8007 (mmp) REVERT: n 32 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8019 (pp) REVERT: n 73 ILE cc_start: 0.8687 (mp) cc_final: 0.8034 (tp) REVERT: n 204 ASP cc_start: 0.8379 (p0) cc_final: 0.7940 (p0) REVERT: e 58 LEU cc_start: 0.8936 (mm) cc_final: 0.8600 (mm) REVERT: e 64 LYS cc_start: 0.8507 (tptm) cc_final: 0.7929 (mtmt) REVERT: e 92 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: e 101 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7297 (mtt180) outliers start: 50 outliers final: 36 residues processed: 225 average time/residue: 0.0762 time to fit residues: 24.6871 Evaluate side-chains 230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 GLN m 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105110 restraints weight = 13419.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108447 restraints weight = 8397.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109650 restraints weight = 5918.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109948 restraints weight = 5123.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110483 restraints weight = 5039.022| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8633 Z= 0.122 Angle : 0.647 9.120 11715 Z= 0.338 Chirality : 0.043 0.221 1309 Planarity : 0.004 0.045 1492 Dihedral : 5.761 50.900 1165 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 3.72 % Allowed : 20.72 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1057 helix: 3.13 (0.30), residues: 257 sheet: 0.15 (0.33), residues: 260 loop : -2.25 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG m 63 TYR 0.017 0.001 TYR b 33 PHE 0.026 0.001 PHE m 55 TRP 0.014 0.001 TRP n 178 HIS 0.007 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8619) covalent geometry : angle 0.63628 (11687) SS BOND : bond 0.00317 ( 14) SS BOND : angle 2.52445 ( 28) hydrogen bonds : bond 0.03443 ( 397) hydrogen bonds : angle 4.25477 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 23 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8530 (mmtt) REVERT: f 86 GLU cc_start: 0.8420 (mp0) cc_final: 0.7968 (mp0) REVERT: f 90 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (mm) REVERT: f 111 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: f 150 TYR cc_start: 0.7434 (m-10) cc_final: 0.7138 (t80) REVERT: g 38 GLU cc_start: 0.7139 (pm20) cc_final: 0.6235 (mp0) REVERT: m 126 THR cc_start: 0.9143 (m) cc_final: 0.8900 (p) REVERT: n 32 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7976 (pp) REVERT: n 73 ILE cc_start: 0.8708 (mp) cc_final: 0.8110 (tp) REVERT: n 204 ASP cc_start: 0.8334 (p0) cc_final: 0.7884 (p0) REVERT: e 58 LEU cc_start: 0.8926 (mm) cc_final: 0.8563 (mm) REVERT: e 64 LYS cc_start: 0.8445 (tptm) cc_final: 0.7805 (mtmt) REVERT: e 92 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: e 101 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7168 (mmt180) outliers start: 35 outliers final: 25 residues processed: 219 average time/residue: 0.0861 time to fit residues: 26.2636 Evaluate side-chains 218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 44 ASN m 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105543 restraints weight = 13609.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108621 restraints weight = 8205.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110203 restraints weight = 5940.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110438 restraints weight = 5052.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110793 restraints weight = 5032.509| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8633 Z= 0.129 Angle : 0.654 9.412 11715 Z= 0.338 Chirality : 0.043 0.236 1309 Planarity : 0.004 0.059 1492 Dihedral : 5.628 48.031 1165 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.29 % Allowed : 21.36 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1057 helix: 3.25 (0.30), residues: 257 sheet: 0.18 (0.33), residues: 259 loop : -2.20 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 101 TYR 0.020 0.001 TYR d 71 PHE 0.036 0.001 PHE n 219 TRP 0.026 0.001 TRP m 57 HIS 0.006 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8619) covalent geometry : angle 0.64671 (11687) SS BOND : bond 0.00306 ( 14) SS BOND : angle 2.08487 ( 28) hydrogen bonds : bond 0.03362 ( 397) hydrogen bonds : angle 4.19778 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8247 (t80) cc_final: 0.7730 (t80) REVERT: d 23 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8455 (mmtt) REVERT: f 86 GLU cc_start: 0.8402 (mp0) cc_final: 0.7930 (mp0) REVERT: f 90 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8205 (mm) REVERT: f 104 LYS cc_start: 0.7531 (tptp) cc_final: 0.7325 (mptt) REVERT: g 38 GLU cc_start: 0.7098 (pm20) cc_final: 0.6214 (mp0) REVERT: n 32 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7989 (pp) REVERT: n 73 ILE cc_start: 0.8730 (mp) cc_final: 0.8142 (tp) REVERT: e 64 LYS cc_start: 0.8402 (tptm) cc_final: 0.7763 (mtmt) REVERT: e 92 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7243 (mp10) outliers start: 31 outliers final: 27 residues processed: 211 average time/residue: 0.0832 time to fit residues: 24.4957 Evaluate side-chains 212 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 GLN m 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105034 restraints weight = 13610.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108564 restraints weight = 8398.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110344 restraints weight = 5881.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110411 restraints weight = 4848.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110733 restraints weight = 4796.544| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8633 Z= 0.147 Angle : 0.655 9.396 11715 Z= 0.341 Chirality : 0.043 0.232 1309 Planarity : 0.004 0.039 1492 Dihedral : 5.624 45.269 1165 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.29 % Allowed : 21.68 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 1057 helix: 3.24 (0.30), residues: 257 sheet: 0.17 (0.33), residues: 265 loop : -2.14 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 102 TYR 0.020 0.001 TYR d 71 PHE 0.029 0.002 PHE n 219 TRP 0.021 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8619) covalent geometry : angle 0.64786 (11687) SS BOND : bond 0.00324 ( 14) SS BOND : angle 2.07836 ( 28) hydrogen bonds : bond 0.03411 ( 397) hydrogen bonds : angle 4.21860 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8247 (t80) cc_final: 0.7771 (t80) REVERT: f 86 GLU cc_start: 0.8403 (mp0) cc_final: 0.7934 (mp0) REVERT: f 90 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8191 (mm) REVERT: g 38 GLU cc_start: 0.7133 (pm20) cc_final: 0.6262 (mp0) REVERT: m 126 THR cc_start: 0.9127 (m) cc_final: 0.8912 (p) REVERT: n 32 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.7996 (pp) REVERT: n 73 ILE cc_start: 0.8732 (mp) cc_final: 0.8139 (tp) REVERT: e 64 LYS cc_start: 0.8360 (tptm) cc_final: 0.7750 (mtmt) outliers start: 31 outliers final: 27 residues processed: 203 average time/residue: 0.0847 time to fit residues: 24.1268 Evaluate side-chains 210 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 93 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 54 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105831 restraints weight = 13566.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108783 restraints weight = 8298.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110320 restraints weight = 5976.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110642 restraints weight = 5111.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111084 restraints weight = 5055.848| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8633 Z= 0.137 Angle : 0.659 9.766 11715 Z= 0.339 Chirality : 0.043 0.233 1309 Planarity : 0.004 0.035 1492 Dihedral : 5.298 44.835 1162 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.51 % Allowed : 21.79 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1057 helix: 3.34 (0.30), residues: 257 sheet: 0.24 (0.33), residues: 258 loop : -2.14 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 102 TYR 0.019 0.001 TYR d 71 PHE 0.026 0.001 PHE n 219 TRP 0.021 0.001 TRP m 57 HIS 0.006 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8619) covalent geometry : angle 0.65351 (11687) SS BOND : bond 0.00340 ( 14) SS BOND : angle 1.86087 ( 28) hydrogen bonds : bond 0.03353 ( 397) hydrogen bonds : angle 4.15830 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1503.21 seconds wall clock time: 26 minutes 34.67 seconds (1594.67 seconds total)