Starting phenix.real_space_refine on Wed Feb 12 22:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_9895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_9895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_9895.map" model { file = "/net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_9895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jxr_9895/02_2025/6jxr_9895.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'ASP: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: 5.12, per 1000 atoms: 0.61 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: 2.12 Conformation dependent library (CDL) restraints added in 941.1 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: 1.14 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: 2.57 Time building geometry restraints manager: 2.47 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: 0.010 Normalize map: mean=0, sd=1: 1.030 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- 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 8619 Z= 0.490 Angle : 1.011 12.938 11687 Z= 0.558 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (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 TRP 0.023 0.003 TRP n 179 HIS 0.008 0.002 HIS n 173 PHE 0.058 0.003 PHE m 157 TYR 0.039 0.003 TYR e 149 ARG 0.007 0.001 ARG n 228 *********************** 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 : 0.932 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: 0.8034 (m) cc_final: 0.7003 (m) outliers start: 7 outliers final: 3 residues processed: 356 average time/residue: 0.2034 time to fit residues: 98.0015 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 : 1.045 ------------------------------------------------------------------------------- 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 86 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 e 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109367 restraints weight = 13241.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112807 restraints weight = 8174.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114257 restraints weight = 5623.018| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8619 Z= 0.222 Angle : 0.711 12.227 11687 Z= 0.369 Chirality : 0.045 0.282 1309 Planarity : 0.005 0.048 1492 Dihedral : 6.826 58.776 1167 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 3.19 % Allowed : 14.03 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1057 helix: 1.11 (0.30), residues: 261 sheet: -1.19 (0.28), residues: 285 loop : -2.93 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 271 HIS 0.003 0.001 HIS n 226 PHE 0.024 0.002 PHE m 157 TYR 0.026 0.002 TYR n 50 ARG 0.007 0.001 ARG m 185 *********************** 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 269 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7183 (t80) cc_final: 0.6608 (t80) REVERT: d 55 ILE cc_start: 0.8088 (tt) cc_final: 0.7802 (tt) REVERT: f 75 ILE cc_start: 0.8809 (mt) cc_final: 0.8567 (mp) REVERT: f 86 GLU cc_start: 0.8343 (mp0) cc_final: 0.7976 (mp0) REVERT: f 111 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: f 122 CYS cc_start: 0.3675 (t) cc_final: 0.3147 (t) REVERT: g 109 GLU cc_start: 0.7210 (mp0) cc_final: 0.6914 (mm-30) REVERT: m 63 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7403 (mmm160) REVERT: m 207 ASN cc_start: 0.8146 (t0) cc_final: 0.7763 (t0) REVERT: m 233 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7054 (mm-30) REVERT: n 32 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8164 (pp) REVERT: n 38 MET cc_start: 0.8477 (tpp) cc_final: 0.7841 (tmm) REVERT: n 204 ASP cc_start: 0.8067 (p0) cc_final: 0.7805 (p0) REVERT: e 64 LYS cc_start: 0.8410 (tptm) cc_final: 0.7914 (mtmt) outliers start: 30 outliers final: 23 residues processed: 255 average time/residue: 0.1932 time to fit residues: 68.4013 Evaluate side-chains 231 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 f residue 146 LEU 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 264 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 75 ASP Chi-restraints excluded: chain n residue 187 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 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.139752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108425 restraints weight = 13285.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111576 restraints weight = 8874.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112742 restraints weight = 6167.613| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8619 Z= 0.249 Angle : 0.662 9.806 11687 Z= 0.346 Chirality : 0.044 0.260 1309 Planarity : 0.004 0.051 1492 Dihedral : 6.698 57.954 1167 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.99 % Allowed : 14.35 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1057 helix: 1.95 (0.31), residues: 261 sheet: -0.60 (0.29), residues: 273 loop : -2.74 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 PHE 0.021 0.001 PHE m 157 TYR 0.028 0.002 TYR n 83 ARG 0.007 0.001 ARG m 269 *********************** 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 266 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 56 GLU cc_start: 0.5743 (tt0) cc_final: 0.5152 (tt0) REVERT: f 86 GLU cc_start: 0.8322 (mp0) cc_final: 0.7936 (mp0) REVERT: f 111 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: g 109 GLU cc_start: 0.7466 (mp0) cc_final: 0.6907 (mp0) REVERT: m 63 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7428 (mmm160) REVERT: m 207 ASN cc_start: 0.8164 (t0) cc_final: 0.7883 (t0) REVERT: n 32 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8121 (pp) REVERT: n 38 MET cc_start: 0.8408 (tpp) cc_final: 0.8003 (tmm) REVERT: n 73 ILE cc_start: 0.8512 (mp) cc_final: 0.7865 (tp) REVERT: n 204 ASP cc_start: 0.8255 (p0) cc_final: 0.7867 (p0) REVERT: e 64 LYS cc_start: 0.8435 (tptm) cc_final: 0.8018 (mtmt) REVERT: e 124 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7355 (mm-30) outliers start: 47 outliers final: 32 residues processed: 251 average time/residue: 0.2058 time to fit residues: 71.8189 Evaluate side-chains 230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 29 LEU 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 f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL 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 255 LEU 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 Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 0.0050 chunk 39 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 52 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.138851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106876 restraints weight = 13192.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111319 restraints weight = 8003.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112460 restraints weight = 5240.014| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8619 Z= 0.165 Angle : 0.619 9.631 11687 Z= 0.322 Chirality : 0.043 0.209 1309 Planarity : 0.004 0.052 1492 Dihedral : 6.225 58.796 1167 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.25 % Allowed : 16.26 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1057 helix: 2.41 (0.31), residues: 263 sheet: -0.26 (0.31), residues: 269 loop : -2.55 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP m 197 HIS 0.005 0.001 HIS f 61 PHE 0.019 0.001 PHE m 157 TYR 0.016 0.001 TYR n 282 ARG 0.010 0.001 ARG m 269 *********************** 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 261 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7244 (t80) cc_final: 0.7036 (t80) REVERT: b 40 PHE cc_start: 0.8017 (t80) cc_final: 0.7679 (t80) REVERT: d 23 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8487 (mmtt) REVERT: d 91 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8425 (ttp80) REVERT: f 86 GLU cc_start: 0.8368 (mp0) cc_final: 0.7945 (mp0) REVERT: f 90 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8141 (mm) REVERT: f 111 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: f 150 TYR cc_start: 0.7523 (m-80) cc_final: 0.7132 (t80) REVERT: g 103 MET cc_start: 0.7298 (mmm) cc_final: 0.6978 (mmm) REVERT: m 183 ASP cc_start: 0.8206 (p0) cc_final: 0.7968 (p0) REVERT: n 73 ILE cc_start: 0.8636 (mp) cc_final: 0.8077 (tp) REVERT: n 204 ASP cc_start: 0.8372 (p0) cc_final: 0.7956 (p0) REVERT: e 64 LYS cc_start: 0.8436 (tptm) cc_final: 0.7921 (mtmt) outliers start: 40 outliers final: 29 residues processed: 246 average time/residue: 0.1971 time to fit residues: 66.4068 Evaluate side-chains 236 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 126 ASP 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 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 33 LYS 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 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 Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 e 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105857 restraints weight = 13350.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109004 restraints weight = 8303.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110163 restraints weight = 5884.951| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8619 Z= 0.213 Angle : 0.623 9.449 11687 Z= 0.327 Chirality : 0.043 0.205 1309 Planarity : 0.004 0.040 1492 Dihedral : 5.878 57.225 1165 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.36 % Allowed : 18.28 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1057 helix: 2.50 (0.31), residues: 269 sheet: -0.07 (0.32), residues: 263 loop : -2.38 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 PHE 0.031 0.001 PHE n 219 TYR 0.015 0.001 TYR d 71 ARG 0.007 0.001 ARG f 117 *********************** 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 252 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8023 (t80) cc_final: 0.7698 (t80) REVERT: d 23 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8473 (mmtt) REVERT: d 72 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8169 (ttm-80) REVERT: f 86 GLU cc_start: 0.8380 (mp0) cc_final: 0.7944 (mp0) REVERT: f 111 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: f 150 TYR cc_start: 0.7527 (m-80) cc_final: 0.7163 (t80) REVERT: g 38 GLU cc_start: 0.6947 (pm20) cc_final: 0.5999 (mp0) REVERT: g 84 MET cc_start: 0.8163 (mmp) cc_final: 0.7932 (mmp) REVERT: n 32 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8109 (pp) REVERT: n 73 ILE cc_start: 0.8636 (mp) cc_final: 0.8109 (tp) REVERT: n 204 ASP cc_start: 0.8336 (p0) cc_final: 0.7921 (p0) REVERT: e 64 LYS cc_start: 0.8534 (tptm) cc_final: 0.7931 (mtmt) REVERT: e 92 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: e 101 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7087 (mtt180) outliers start: 41 outliers final: 25 residues processed: 236 average time/residue: 0.1911 time to fit residues: 62.6918 Evaluate side-chains 226 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 29 LEU 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 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 33 LYS 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 63 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.139078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107610 restraints weight = 13200.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111153 restraints weight = 8292.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112362 restraints weight = 5763.774| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8619 Z= 0.161 Angle : 0.603 9.342 11687 Z= 0.316 Chirality : 0.042 0.210 1309 Planarity : 0.004 0.032 1492 Dihedral : 5.702 57.182 1165 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.83 % Allowed : 19.02 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1057 helix: 2.94 (0.31), residues: 263 sheet: 0.13 (0.32), residues: 263 loop : -2.34 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.005 0.001 HIS f 61 PHE 0.023 0.001 PHE n 219 TYR 0.016 0.001 TYR d 71 ARG 0.005 0.001 ARG m 63 *********************** 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 243 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7936 (t80) cc_final: 0.7651 (t80) REVERT: d 28 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7809 (mt-10) REVERT: f 86 GLU cc_start: 0.8386 (mp0) cc_final: 0.7947 (mp0) REVERT: f 128 MET cc_start: 0.6678 (ppp) cc_final: 0.6206 (ppp) REVERT: n 32 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8126 (pp) REVERT: n 73 ILE cc_start: 0.8648 (mp) cc_final: 0.8121 (tp) REVERT: n 204 ASP cc_start: 0.8310 (p0) cc_final: 0.7876 (p0) REVERT: n 263 ASP cc_start: 0.7729 (p0) cc_final: 0.7518 (p0) REVERT: e 64 LYS cc_start: 0.8391 (tptm) cc_final: 0.7892 (mtmt) REVERT: e 92 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7337 (mp10) outliers start: 36 outliers final: 26 residues processed: 227 average time/residue: 0.1910 time to fit residues: 60.3535 Evaluate side-chains 213 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE 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 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 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 33 LYS 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 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 43 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106153 restraints weight = 13447.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109105 restraints weight = 8445.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110181 restraints weight = 6091.403| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8619 Z= 0.227 Angle : 0.626 9.125 11687 Z= 0.328 Chirality : 0.043 0.211 1309 Planarity : 0.004 0.032 1492 Dihedral : 5.738 53.458 1165 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.25 % Allowed : 19.45 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1057 helix: 3.01 (0.30), residues: 262 sheet: 0.21 (0.32), residues: 263 loop : -2.29 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 178 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.002 PHE n 219 TYR 0.017 0.001 TYR d 71 ARG 0.005 0.001 ARG d 91 *********************** 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 232 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7962 (t80) cc_final: 0.7689 (t80) REVERT: f 86 GLU cc_start: 0.8450 (mp0) cc_final: 0.7986 (mp0) REVERT: f 128 MET cc_start: 0.6840 (ppp) cc_final: 0.6388 (ppp) REVERT: g 38 GLU cc_start: 0.6929 (pm20) cc_final: 0.6129 (mp0) REVERT: g 84 MET cc_start: 0.8120 (mmp) cc_final: 0.7883 (mmp) REVERT: m 55 PHE cc_start: 0.8542 (m-10) cc_final: 0.8172 (m-10) REVERT: n 32 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8018 (pp) REVERT: n 73 ILE cc_start: 0.8605 (mp) cc_final: 0.8092 (tp) REVERT: e 64 LYS cc_start: 0.8457 (tptm) cc_final: 0.7903 (mtmt) REVERT: e 92 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7357 (mp10) outliers start: 40 outliers final: 30 residues processed: 215 average time/residue: 0.1821 time to fit residues: 55.5444 Evaluate side-chains 218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 97 VAL 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 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 33 LYS 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 146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103721 restraints weight = 13660.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105921 restraints weight = 9519.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107607 restraints weight = 6899.608| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8619 Z= 0.297 Angle : 0.668 9.132 11687 Z= 0.349 Chirality : 0.044 0.224 1309 Planarity : 0.004 0.035 1492 Dihedral : 5.802 45.526 1165 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.46 % Allowed : 19.66 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1057 helix: 2.87 (0.30), residues: 264 sheet: 0.05 (0.32), residues: 274 loop : -2.33 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 PHE 0.021 0.002 PHE m 157 TYR 0.017 0.002 TYR d 71 ARG 0.005 0.001 ARG d 91 *********************** 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 224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8037 (t80) cc_final: 0.7794 (t80) REVERT: f 86 GLU cc_start: 0.8462 (mp0) cc_final: 0.7982 (mp0) REVERT: f 111 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: m 55 PHE cc_start: 0.8557 (m-10) cc_final: 0.8148 (m-10) REVERT: m 94 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9096 (pt) REVERT: n 32 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8009 (pp) REVERT: n 73 ILE cc_start: 0.8648 (mp) cc_final: 0.8089 (tp) REVERT: e 64 LYS cc_start: 0.8467 (tptm) cc_final: 0.7916 (mtmt) REVERT: e 89 GLU cc_start: 0.7133 (tt0) cc_final: 0.6868 (tt0) outliers start: 42 outliers final: 32 residues processed: 205 average time/residue: 0.1894 time to fit residues: 54.2437 Evaluate side-chains 213 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL 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 94 ILE 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 33 LYS 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 97 VAL Chi-restraints excluded: chain e residue 126 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 31 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: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN e 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104223 restraints weight = 13675.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107656 restraints weight = 8320.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109947 restraints weight = 6077.095| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8619 Z= 0.206 Angle : 0.640 9.047 11687 Z= 0.333 Chirality : 0.043 0.221 1309 Planarity : 0.004 0.033 1492 Dihedral : 5.389 43.625 1162 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.25 % Allowed : 20.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1057 helix: 3.07 (0.30), residues: 263 sheet: 0.12 (0.32), residues: 267 loop : -2.21 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.018 0.001 PHE a 40 TYR 0.019 0.001 TYR d 71 ARG 0.004 0.001 ARG m 63 *********************** 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 228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7978 (t80) cc_final: 0.7740 (t80) REVERT: f 86 GLU cc_start: 0.8439 (mp0) cc_final: 0.7985 (mp0) REVERT: f 111 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: g 38 GLU cc_start: 0.6842 (pm20) cc_final: 0.6043 (mp0) REVERT: n 32 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8017 (pp) REVERT: n 73 ILE cc_start: 0.8634 (mp) cc_final: 0.8087 (tp) REVERT: e 64 LYS cc_start: 0.8421 (tptm) cc_final: 0.7824 (mtmt) outliers start: 40 outliers final: 33 residues processed: 211 average time/residue: 0.1954 time to fit residues: 57.2090 Evaluate side-chains 216 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 32 CYS 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 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 97 VAL 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 148 VAL 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 33 LYS Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 106 SER 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 97 VAL Chi-restraints excluded: chain e residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105159 restraints weight = 13572.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107896 restraints weight = 9844.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109241 restraints weight = 7034.967| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8619 Z= 0.223 Angle : 0.661 10.135 11687 Z= 0.340 Chirality : 0.043 0.230 1309 Planarity : 0.004 0.066 1492 Dihedral : 5.388 43.208 1162 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.93 % Allowed : 21.57 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1057 helix: 3.07 (0.30), residues: 263 sheet: 0.21 (0.32), residues: 268 loop : -2.17 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.025 0.002 PHE m 55 TYR 0.019 0.001 TYR d 71 ARG 0.008 0.001 ARG f 117 ********************** 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 220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7974 (t80) cc_final: 0.7773 (t80) REVERT: f 86 GLU cc_start: 0.8391 (mp0) cc_final: 0.7953 (mp0) REVERT: f 111 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: g 38 GLU cc_start: 0.7099 (pm20) cc_final: 0.6351 (mp0) REVERT: n 32 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.7983 (pp) REVERT: n 73 ILE cc_start: 0.8635 (mp) cc_final: 0.8069 (tp) REVERT: e 64 LYS cc_start: 0.8486 (tptm) cc_final: 0.7851 (mtmt) outliers start: 37 outliers final: 32 residues processed: 203 average time/residue: 0.1899 time to fit residues: 53.8191 Evaluate side-chains 212 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 32 CYS 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 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 97 VAL 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 148 VAL 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 33 LYS 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 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 97 VAL Chi-restraints excluded: chain e residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 72 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** g 29 HIS m 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105934 restraints weight = 13651.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108311 restraints weight = 9824.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109693 restraints weight = 7214.215| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8619 Z= 0.207 Angle : 0.656 9.246 11687 Z= 0.337 Chirality : 0.043 0.228 1309 Planarity : 0.004 0.083 1492 Dihedral : 5.357 43.131 1162 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.61 % Allowed : 21.79 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1057 helix: 3.13 (0.30), residues: 263 sheet: 0.14 (0.32), residues: 275 loop : -2.16 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.024 0.002 PHE m 55 TYR 0.020 0.001 TYR d 71 ARG 0.012 0.001 ARG f 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.95 seconds wall clock time: 50 minutes 59.18 seconds (3059.18 seconds total)