Starting phenix.real_space_refine on Sat Jul 26 06:08:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jxr_9895/07_2025/6jxr_9895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jxr_9895/07_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_9895/07_2025/6jxr_9895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jxr_9895/07_2025/6jxr_9895.map" model { file = "/net/cci-nas-00/data/ceres_data/6jxr_9895/07_2025/6jxr_9895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jxr_9895/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.36, per 1000 atoms: 0.64 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.13 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: 2.48 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2693 1.34 - 1.46: 2032 1.46 - 1.59: 3817 1.59 - 1.71: 1 1.71 - 1.83: 76 Bond restraints: 8619 Sorted by residual: bond pdb=" CE LYS m 190 " pdb=" NZ LYS m 190 " ideal model delta sigma weight residual 1.489 1.620 -0.131 3.00e-02 1.11e+03 1.90e+01 bond pdb=" CB VAL d 33 " pdb=" CG2 VAL d 33 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.78e+00 bond pdb=" C PHE n 147 " pdb=" N GLU n 148 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" CB VAL m 154 " pdb=" CG2 VAL m 154 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CG ARG d 57 " pdb=" CD ARG d 57 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 ... (remaining 8614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 11382 2.59 - 5.18: 257 5.18 - 7.76: 35 7.76 - 10.35: 9 10.35 - 12.94: 4 Bond angle restraints: 11687 Sorted by residual: angle pdb=" C THR m 158 " pdb=" N ASP m 159 " pdb=" CA ASP m 159 " ideal model delta sigma weight residual 121.54 134.48 -12.94 1.91e+00 2.74e-01 4.59e+01 angle pdb=" C LEU b 27 " pdb=" N ASP b 28 " pdb=" CA ASP b 28 " ideal model delta sigma weight residual 121.62 130.41 -8.79 1.57e+00 4.06e-01 3.13e+01 angle pdb=" N PHE n 219 " pdb=" CA PHE n 219 " pdb=" C PHE n 219 " ideal model delta sigma weight residual 114.04 107.14 6.90 1.24e+00 6.50e-01 3.10e+01 angle pdb=" C THR d 76 " pdb=" N ASP d 77 " pdb=" CA ASP d 77 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PHE m 160 " pdb=" CA PHE m 160 " pdb=" C PHE m 160 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 ... (remaining 11682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 4882 15.70 - 31.40: 204 31.40 - 47.10: 65 47.10 - 62.80: 15 62.80 - 78.50: 10 Dihedral angle restraints: 5176 sinusoidal: 2056 harmonic: 3120 Sorted by residual: dihedral pdb=" CA ASP m 217 " pdb=" C ASP m 217 " pdb=" N THR m 218 " pdb=" CA THR m 218 " ideal model delta harmonic sigma weight residual 180.00 129.80 50.20 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ILE b 38 " pdb=" C ILE b 38 " pdb=" N LEU b 39 " pdb=" CA LEU b 39 " ideal model delta harmonic sigma weight residual 180.00 132.28 47.72 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ASP m 159 " pdb=" C ASP m 159 " pdb=" N PHE m 160 " pdb=" CA PHE m 160 " ideal model delta harmonic sigma weight residual 180.00 144.29 35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1040 0.068 - 0.135: 241 0.135 - 0.203: 22 0.203 - 0.270: 5 0.270 - 0.338: 1 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CB ILE d 78 " pdb=" CA ILE d 78 " pdb=" CG1 ILE d 78 " pdb=" CG2 ILE d 78 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR d 79 " pdb=" N TYR d 79 " pdb=" C TYR d 79 " pdb=" CB TYR d 79 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1306 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE m 157 " -0.022 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE m 157 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE m 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE m 157 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE m 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE m 157 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE m 157 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO n 223 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE n 140 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO n 141 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO n 141 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO n 141 " 0.036 5.00e-02 4.00e+02 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2100 2.80 - 3.32: 7266 3.32 - 3.85: 13211 3.85 - 4.37: 14744 4.37 - 4.90: 26395 Nonbonded interactions: 63716 Sorted by model distance: nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.273 3.040 nonbonded pdb=" O THR d 47 " pdb=" OH TYR d 71 " model vdw 2.289 3.040 nonbonded pdb=" NH1 ARG d 57 " pdb=" O ARG m 185 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASP g 35 " pdb=" OH TYR g 101 " model vdw 2.303 3.040 nonbonded pdb=" O PHE m 160 " pdb=" OG1 THR m 164 " model vdw 2.313 3.040 ... (remaining 63711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 24 through 55) selection = chain 'b' } ncs_group { reference = chain 'e' selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.340 Find NCS groups from input model: 0.190 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 8633 Z= 0.329 Angle : 1.015 12.938 11715 Z= 0.560 Chirality : 0.057 0.338 1309 Planarity : 0.007 0.076 1492 Dihedral : 10.827 78.503 3132 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 0.74 % Allowed : 3.72 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.12255 ( 397) hydrogen bonds : angle 6.13083 ( 1083) SS BOND : bond 0.00522 ( 14) SS BOND : angle 2.05565 ( 28) covalent geometry : bond 0.00751 ( 8619) covalent geometry : angle 1.01077 (11687) *********************** 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 : 0.967 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: 0.1963 time to fit residues: 94.8664 Evaluate side-chains 211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.0040 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.7874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 94 GLN f 92 GLN g 28 ASN m 28 GLN m 199 ASN m 211 ASN n 122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109020 restraints weight = 13251.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112414 restraints weight = 8164.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113853 restraints weight = 5642.491| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8633 Z= 0.154 Angle : 0.714 12.277 11715 Z= 0.370 Chirality : 0.046 0.284 1309 Planarity : 0.005 0.049 1492 Dihedral : 6.814 58.578 1167 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 3.08 % Allowed : 13.92 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (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: -2.09 (0.24), residues: 1057 helix: 1.08 (0.30), residues: 261 sheet: -1.19 (0.28), residues: 285 loop : -2.94 (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 0.024 0.002 TYR n 50 ARG 0.006 0.001 ARG m 185 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 397) hydrogen bonds : angle 4.93983 ( 1083) SS BOND : bond 0.00468 ( 14) SS BOND : angle 1.63607 ( 28) covalent geometry : bond 0.00351 ( 8619) covalent geometry : angle 0.71038 (11687) *********************** 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 267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7206 (t80) cc_final: 0.6590 (t80) REVERT: f 56 GLU cc_start: 0.6032 (tt0) cc_final: 0.5513 (tt0) REVERT: f 75 ILE cc_start: 0.8818 (mt) cc_final: 0.8575 (mp) REVERT: f 86 GLU cc_start: 0.8344 (mp0) cc_final: 0.7980 (mp0) REVERT: f 111 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: f 122 CYS cc_start: 0.3701 (t) cc_final: 0.3177 (t) REVERT: g 109 GLU cc_start: 0.7422 (mp0) cc_final: 0.7176 (mm-30) REVERT: m 63 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7408 (mmm160) REVERT: m 207 ASN cc_start: 0.8110 (t0) cc_final: 0.7745 (t0) REVERT: m 233 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7085 (mm-30) REVERT: n 32 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8162 (pp) REVERT: n 33 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7806 (ttmt) REVERT: n 38 MET cc_start: 0.8482 (tpp) cc_final: 0.7868 (tmm) REVERT: n 204 ASP cc_start: 0.8071 (p0) cc_final: 0.7813 (p0) REVERT: n 306 LYS cc_start: 0.6561 (mmmt) cc_final: 0.6356 (mptt) REVERT: e 64 LYS cc_start: 0.8370 (tptm) cc_final: 0.7904 (mtmt) outliers start: 29 outliers final: 22 residues processed: 254 average time/residue: 0.1960 time to fit residues: 69.2115 Evaluate side-chains 233 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 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: 0.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 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: 2.9990 chunk 52 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106469 restraints weight = 13379.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109454 restraints weight = 8174.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110642 restraints weight = 5865.663| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8633 Z= 0.171 Angle : 0.674 9.840 11715 Z= 0.351 Chirality : 0.044 0.254 1309 Planarity : 0.004 0.042 1492 Dihedral : 6.701 56.420 1167 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.78 % Allowed : 15.30 % Favored : 79.91 % 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: -1.41 (0.25), residues: 1057 helix: 1.89 (0.31), residues: 261 sheet: -0.60 (0.29), residues: 273 loop : -2.76 (0.23), 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 0.023 0.001 PHE m 157 TYR 0.023 0.002 TYR n 83 ARG 0.008 0.001 ARG m 269 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 397) hydrogen bonds : angle 4.67354 ( 1083) SS BOND : bond 0.00351 ( 14) SS BOND : angle 2.17215 ( 28) covalent geometry : bond 0.00390 ( 8619) covalent geometry : angle 0.66589 (11687) *********************** 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 264 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 86 GLU cc_start: 0.8372 (mp0) cc_final: 0.7964 (mp0) REVERT: f 101 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7904 (tpp80) REVERT: f 111 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: f 123 MET cc_start: 0.5915 (mtt) cc_final: 0.5683 (mtt) REVERT: g 109 GLU cc_start: 0.7477 (mp0) cc_final: 0.6884 (mp0) REVERT: m 63 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7473 (mmm160) REVERT: m 207 ASN cc_start: 0.8242 (t0) cc_final: 0.7963 (t0) REVERT: m 233 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7547 (mm-30) REVERT: n 32 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8113 (pp) REVERT: n 38 MET cc_start: 0.8441 (tpp) cc_final: 0.7959 (tmm) REVERT: n 73 ILE cc_start: 0.8551 (mp) cc_final: 0.7891 (tp) REVERT: n 204 ASP cc_start: 0.8311 (p0) cc_final: 0.7933 (p0) REVERT: e 64 LYS cc_start: 0.8447 (tptm) cc_final: 0.7997 (mtmt) REVERT: e 124 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7332 (mm-30) outliers start: 45 outliers final: 32 residues processed: 250 average time/residue: 0.2438 time to fit residues: 87.8452 Evaluate side-chains 231 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 45 ILE 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 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: 0.9990 chunk 65 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 42 optimal weight: 0.0270 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.138773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107202 restraints weight = 13238.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110595 restraints weight = 8062.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111956 restraints weight = 5646.356| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8633 Z= 0.114 Angle : 0.625 9.513 11715 Z= 0.324 Chirality : 0.043 0.197 1309 Planarity : 0.004 0.051 1492 Dihedral : 6.168 57.753 1167 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.57 % Allowed : 16.47 % Favored : 78.96 % 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: -0.91 (0.25), residues: 1057 helix: 2.40 (0.31), residues: 263 sheet: -0.23 (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 0.016 0.001 PHE m 157 TYR 0.018 0.001 TYR n 83 ARG 0.009 0.001 ARG m 269 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 397) hydrogen bonds : angle 4.37490 ( 1083) SS BOND : bond 0.00305 ( 14) SS BOND : angle 1.96506 ( 28) covalent geometry : bond 0.00248 ( 8619) covalent geometry : angle 0.61841 (11687) *********************** 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 267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7207 (t80) cc_final: 0.7001 (t80) REVERT: b 40 PHE cc_start: 0.8010 (t80) cc_final: 0.7660 (t80) REVERT: d 23 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8612 (mmtt) REVERT: f 86 GLU cc_start: 0.8372 (mp0) cc_final: 0.7947 (mp0) REVERT: f 90 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8122 (mm) REVERT: f 111 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: f 150 TYR cc_start: 0.7508 (m-80) cc_final: 0.7136 (t80) REVERT: g 38 GLU cc_start: 0.6799 (pm20) cc_final: 0.6096 (mt-10) REVERT: g 84 MET cc_start: 0.8116 (mmp) cc_final: 0.7860 (mmp) REVERT: m 183 ASP cc_start: 0.8200 (p0) cc_final: 0.7974 (p0) REVERT: n 73 ILE cc_start: 0.8689 (mp) cc_final: 0.8056 (tp) REVERT: n 204 ASP cc_start: 0.8356 (p0) cc_final: 0.7948 (p0) REVERT: n 306 LYS cc_start: 0.6419 (mmmt) cc_final: 0.6131 (mptt) REVERT: e 64 LYS cc_start: 0.8451 (tptm) cc_final: 0.7934 (mtmt) outliers start: 43 outliers final: 25 residues processed: 252 average time/residue: 0.2447 time to fit residues: 85.7155 Evaluate side-chains 227 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 40 SER Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 268 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 103 SER Chi-restraints excluded: chain e residue 122 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.137342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106039 restraints weight = 13409.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109802 restraints weight = 8231.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111587 restraints weight = 5603.237| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8633 Z= 0.138 Angle : 0.624 9.509 11715 Z= 0.325 Chirality : 0.043 0.206 1309 Planarity : 0.004 0.040 1492 Dihedral : 5.790 55.371 1165 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 18.60 % Favored : 77.68 % 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: -0.65 (0.26), residues: 1057 helix: 2.50 (0.31), residues: 269 sheet: -0.02 (0.32), residues: 261 loop : -2.38 (0.24), residues: 527 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 0.021 0.001 PHE m 157 TYR 0.015 0.001 TYR n 282 ARG 0.007 0.001 ARG m 63 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 397) hydrogen bonds : angle 4.28320 ( 1083) SS BOND : bond 0.00354 ( 14) SS BOND : angle 1.48894 ( 28) covalent geometry : bond 0.00312 ( 8619) covalent geometry : angle 0.62056 (11687) *********************** 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 236 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8004 (t80) cc_final: 0.7678 (t80) REVERT: d 23 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8512 (mmtt) REVERT: f 86 GLU cc_start: 0.8372 (mp0) cc_final: 0.7935 (mp0) REVERT: f 106 GLU cc_start: 0.6749 (pm20) cc_final: 0.6285 (pm20) REVERT: f 111 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: f 150 TYR cc_start: 0.7518 (m-80) cc_final: 0.7180 (t80) REVERT: g 30 LEU cc_start: 0.8188 (mp) cc_final: 0.7981 (mp) REVERT: g 47 ASP cc_start: 0.7197 (m-30) cc_final: 0.6894 (p0) REVERT: n 32 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8113 (pp) REVERT: n 73 ILE cc_start: 0.8631 (mp) cc_final: 0.8082 (tp) REVERT: n 204 ASP cc_start: 0.8300 (p0) cc_final: 0.7896 (p0) REVERT: n 306 LYS cc_start: 0.6542 (mmmt) cc_final: 0.6215 (mptt) REVERT: e 64 LYS cc_start: 0.8509 (tptm) cc_final: 0.7948 (mtmt) REVERT: e 92 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: e 101 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7073 (mmt180) outliers start: 35 outliers final: 24 residues processed: 221 average time/residue: 0.3333 time to fit residues: 105.3660 Evaluate side-chains 224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 26 ILE 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 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 255 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 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: 4.9990 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105998 restraints weight = 13323.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110667 restraints weight = 8053.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111739 restraints weight = 5301.937| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8633 Z= 0.125 Angle : 0.615 9.062 11715 Z= 0.321 Chirality : 0.043 0.209 1309 Planarity : 0.004 0.032 1492 Dihedral : 5.690 53.313 1165 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.83 % Allowed : 19.23 % Favored : 76.94 % 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: -0.43 (0.26), residues: 1057 helix: 2.74 (0.31), residues: 269 sheet: 0.13 (0.32), residues: 261 loop : -2.29 (0.25), residues: 527 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 0.021 0.001 PHE m 262 TYR 0.015 0.001 TYR d 71 ARG 0.005 0.000 ARG m 63 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 397) hydrogen bonds : angle 4.20575 ( 1083) SS BOND : bond 0.00281 ( 14) SS BOND : angle 1.90079 ( 28) covalent geometry : bond 0.00279 ( 8619) covalent geometry : angle 0.60848 (11687) *********************** 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 239 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7951 (t80) cc_final: 0.7665 (t80) REVERT: d 23 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8456 (mmtt) REVERT: d 28 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7854 (mt-10) REVERT: f 86 GLU cc_start: 0.8401 (mp0) cc_final: 0.7947 (mp0) REVERT: g 47 ASP cc_start: 0.7312 (m-30) cc_final: 0.6979 (p0) REVERT: g 84 MET cc_start: 0.8164 (mmp) cc_final: 0.7795 (mmp) REVERT: m 183 ASP cc_start: 0.8331 (p0) cc_final: 0.8089 (p0) REVERT: n 32 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8131 (pp) REVERT: n 73 ILE cc_start: 0.8656 (mp) cc_final: 0.8125 (tp) REVERT: n 204 ASP cc_start: 0.8343 (p0) cc_final: 0.7908 (p0) REVERT: n 306 LYS cc_start: 0.6517 (mmmt) cc_final: 0.6178 (mptt) REVERT: e 64 LYS cc_start: 0.8454 (tptm) cc_final: 0.7900 (mtmt) REVERT: e 92 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7325 (mp10) outliers start: 36 outliers final: 27 residues processed: 225 average time/residue: 0.2110 time to fit residues: 65.2259 Evaluate side-chains 213 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 93 CYS 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 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 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.136415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104190 restraints weight = 13535.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107599 restraints weight = 8699.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109023 restraints weight = 6072.098| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8633 Z= 0.164 Angle : 0.640 9.130 11715 Z= 0.334 Chirality : 0.043 0.213 1309 Planarity : 0.004 0.037 1492 Dihedral : 5.684 48.285 1165 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.68 % Allowed : 18.92 % Favored : 76.41 % 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: -0.36 (0.26), residues: 1057 helix: 2.99 (0.31), residues: 262 sheet: 0.13 (0.32), residues: 263 loop : -2.27 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 PHE 0.032 0.002 PHE n 219 TYR 0.017 0.001 TYR d 71 ARG 0.005 0.001 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 397) hydrogen bonds : angle 4.25650 ( 1083) SS BOND : bond 0.00388 ( 14) SS BOND : angle 1.87828 ( 28) covalent geometry : bond 0.00380 ( 8619) covalent geometry : angle 0.63391 (11687) *********************** 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 239 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8027 (t80) cc_final: 0.7742 (t80) REVERT: d 23 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8509 (mmtt) REVERT: f 86 GLU cc_start: 0.8432 (mp0) cc_final: 0.7985 (mp0) REVERT: f 111 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: g 38 GLU cc_start: 0.6797 (pm20) cc_final: 0.6132 (mp0) REVERT: g 47 ASP cc_start: 0.7281 (m-30) cc_final: 0.6893 (p0) REVERT: m 55 PHE cc_start: 0.8606 (m-10) cc_final: 0.8269 (m-10) REVERT: m 94 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9079 (pt) REVERT: m 126 THR cc_start: 0.9218 (m) cc_final: 0.8967 (p) REVERT: n 32 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8033 (pp) REVERT: n 73 ILE cc_start: 0.8681 (mp) cc_final: 0.8123 (tp) REVERT: e 64 LYS cc_start: 0.8450 (tptm) cc_final: 0.7854 (mtmt) REVERT: e 92 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7342 (mt0) outliers start: 44 outliers final: 30 residues processed: 223 average time/residue: 0.1851 time to fit residues: 57.7951 Evaluate side-chains 218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 94 ILE Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 205 CYS 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 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 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** ** 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 = 0.3824 r_free = 0.3824 target = 0.140684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108730 restraints weight = 13358.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111703 restraints weight = 8331.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113065 restraints weight = 6002.176| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8633 Z= 0.130 Angle : 0.638 8.963 11715 Z= 0.330 Chirality : 0.042 0.218 1309 Planarity : 0.004 0.034 1492 Dihedral : 5.571 45.086 1165 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.14 % Allowed : 19.87 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (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: -0.26 (0.26), residues: 1057 helix: 3.08 (0.31), residues: 264 sheet: 0.18 (0.33), residues: 263 loop : -2.23 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.023 0.001 PHE n 219 TYR 0.017 0.001 TYR d 71 ARG 0.004 0.001 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 397) hydrogen bonds : angle 4.18628 ( 1083) SS BOND : bond 0.00296 ( 14) SS BOND : angle 2.59011 ( 28) covalent geometry : bond 0.00298 ( 8619) covalent geometry : angle 0.62598 (11687) *********************** 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 228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7966 (t80) cc_final: 0.7705 (t80) REVERT: f 86 GLU cc_start: 0.8425 (mp0) cc_final: 0.7945 (mp0) REVERT: g 84 MET cc_start: 0.8130 (mmp) cc_final: 0.7764 (mmp) REVERT: n 32 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7984 (pp) REVERT: n 73 ILE cc_start: 0.8673 (mp) cc_final: 0.8113 (tp) REVERT: e 64 LYS cc_start: 0.8438 (tptm) cc_final: 0.7916 (mtmt) outliers start: 39 outliers final: 34 residues processed: 209 average time/residue: 0.2555 time to fit residues: 75.2042 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 : 1.015 ------------------------------------------------------------------------------- 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 40 SER Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 124 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 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 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.138084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105721 restraints weight = 13714.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109160 restraints weight = 7999.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110430 restraints weight = 5597.194| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8633 Z= 0.126 Angle : 0.632 9.262 11715 Z= 0.327 Chirality : 0.043 0.211 1309 Planarity : 0.004 0.052 1492 Dihedral : 5.233 44.066 1162 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.25 % Allowed : 19.87 % Favored : 75.88 % 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: -0.20 (0.26), residues: 1057 helix: 3.15 (0.31), residues: 263 sheet: 0.15 (0.32), residues: 269 loop : -2.18 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.022 0.001 PHE m 55 TYR 0.018 0.001 TYR d 71 ARG 0.005 0.001 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 397) hydrogen bonds : angle 4.15036 ( 1083) SS BOND : bond 0.00354 ( 14) SS BOND : angle 1.56029 ( 28) covalent geometry : bond 0.00286 ( 8619) covalent geometry : angle 0.62800 (11687) *********************** 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 237 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7968 (t80) cc_final: 0.7703 (t80) REVERT: f 56 GLU cc_start: 0.6212 (pt0) cc_final: 0.4216 (pt0) REVERT: f 86 GLU cc_start: 0.8415 (mp0) cc_final: 0.7957 (mp0) REVERT: f 150 TYR cc_start: 0.6745 (t80) cc_final: 0.6474 (t80) REVERT: g 38 GLU cc_start: 0.6769 (pm20) cc_final: 0.5945 (mp0) REVERT: g 84 MET cc_start: 0.8190 (mmp) cc_final: 0.7813 (mmp) REVERT: n 32 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8046 (pp) REVERT: n 73 ILE cc_start: 0.8684 (mp) cc_final: 0.8131 (tp) REVERT: n 204 ASP cc_start: 0.8366 (p0) cc_final: 0.7934 (p0) REVERT: e 64 LYS cc_start: 0.8442 (tptm) cc_final: 0.7846 (mtmt) outliers start: 40 outliers final: 34 residues processed: 221 average time/residue: 0.2756 time to fit residues: 85.6751 Evaluate side-chains 217 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 124 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 g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 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 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: 3.9990 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 28 GLN ** 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 = 0.3795 r_free = 0.3795 target = 0.138245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106922 restraints weight = 13484.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109928 restraints weight = 8266.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111549 restraints weight = 5981.509| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8633 Z= 0.139 Angle : 0.654 10.002 11715 Z= 0.339 Chirality : 0.044 0.287 1309 Planarity : 0.004 0.064 1492 Dihedral : 5.275 43.699 1162 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.72 % Allowed : 21.04 % Favored : 75.24 % 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: -0.15 (0.26), residues: 1057 helix: 3.14 (0.30), residues: 263 sheet: 0.21 (0.32), residues: 270 loop : -2.13 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.049 0.002 PHE n 219 TYR 0.019 0.001 TYR d 71 ARG 0.008 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 397) hydrogen bonds : angle 4.14985 ( 1083) SS BOND : bond 0.00304 ( 14) SS BOND : angle 1.62055 ( 28) covalent geometry : bond 0.00319 ( 8619) covalent geometry : angle 0.65030 (11687) ********************** 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 222 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7946 (t80) cc_final: 0.7738 (t80) REVERT: d 27 GLU cc_start: 0.8167 (pt0) cc_final: 0.7924 (pt0) REVERT: f 59 TRP cc_start: 0.8418 (m100) cc_final: 0.8074 (m100) REVERT: f 86 GLU cc_start: 0.8401 (mp0) cc_final: 0.7950 (mp0) REVERT: f 104 LYS cc_start: 0.7885 (tptp) cc_final: 0.7171 (tptm) REVERT: g 38 GLU cc_start: 0.6950 (pm20) cc_final: 0.6263 (mp0) REVERT: n 32 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7977 (pp) REVERT: n 73 ILE cc_start: 0.8683 (mp) cc_final: 0.8123 (tp) REVERT: n 204 ASP cc_start: 0.8356 (p0) cc_final: 0.7917 (p0) REVERT: e 64 LYS cc_start: 0.8393 (tptm) cc_final: 0.7820 (mtmt) outliers start: 35 outliers final: 34 residues processed: 209 average time/residue: 0.1897 time to fit residues: 55.3286 Evaluate side-chains 217 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 124 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 g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 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 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: 5.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107407 restraints weight = 13583.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110649 restraints weight = 8209.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112167 restraints weight = 5946.964| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8633 Z= 0.135 Angle : 0.653 9.291 11715 Z= 0.339 Chirality : 0.044 0.273 1309 Planarity : 0.004 0.059 1492 Dihedral : 5.276 43.747 1162 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.72 % Allowed : 21.36 % Favored : 74.92 % 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: -0.10 (0.26), residues: 1057 helix: 3.18 (0.30), residues: 263 sheet: 0.20 (0.32), residues: 269 loop : -2.07 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP m 57 HIS 0.005 0.001 HIS f 61 PHE 0.043 0.002 PHE n 219 TYR 0.019 0.001 TYR d 71 ARG 0.010 0.001 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 397) hydrogen bonds : angle 4.13256 ( 1083) SS BOND : bond 0.00270 ( 14) SS BOND : angle 1.42348 ( 28) covalent geometry : bond 0.00311 ( 8619) covalent geometry : angle 0.65032 (11687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.94 seconds wall clock time: 63 minutes 16.18 seconds (3796.18 seconds total)