Starting phenix.real_space_refine on Tue Mar 3 17:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2026/7tuy_26135.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 Cl 3 4.86 5 C 4575 2.51 5 N 1201 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7157 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 8 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KKF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7157 At special positions: 0 Unit cell: (64.74, 100.43, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 36 16.00 O 1342 8.00 N 1201 7.00 C 4575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 287.8 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 37.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.685A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 201 through 206 removed outlier: 4.010A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.514A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 189' Processing helix chain 'R' and resid 26 through 59 removed outlier: 3.901A pdb=" N ILE R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 66 through 83 Processing helix chain 'R' and resid 101 through 133 removed outlier: 4.031A pdb=" N ALA R 117 " --> pdb=" O ILE R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 143 Processing helix chain 'R' and resid 144 through 164 removed outlier: 3.679A pdb=" N ALA R 148 " --> pdb=" O ARG R 144 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU R 164 " --> pdb=" O PHE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 168 removed outlier: 4.248A pdb=" N ILE R 168 " --> pdb=" O PRO R 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 165 through 168' Processing helix chain 'R' and resid 195 through 205 removed outlier: 4.160A pdb=" N GLY R 199 " --> pdb=" O TRP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 1002 through 1025 Processing helix chain 'R' and resid 1030 through 1046 removed outlier: 3.620A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP R1044 " --> pdb=" O ALA R1040 " (cutoff:3.500A) Processing helix chain 'R' and resid 1062 through 1087 removed outlier: 3.547A pdb=" N GLY R1069 " --> pdb=" O ASP R1065 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) Processing helix chain 'R' and resid 1090 through 1092 No H-bonds generated for 'chain 'R' and resid 1090 through 1092' Processing helix chain 'R' and resid 1094 through 1107 removed outlier: 4.051A pdb=" N GLN R1098 " --> pdb=" O ALA R1094 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU R1099 " --> pdb=" O ALA R1095 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS R1100 " --> pdb=" O ALA R1096 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR R1101 " --> pdb=" O GLU R1097 " (cutoff:3.500A) Processing helix chain 'R' and resid 1107 through 1117 removed outlier: 4.081A pdb=" N GLU R1112 " --> pdb=" O GLN R1108 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG R1113 " --> pdb=" O LYS R1109 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 247 Processing helix chain 'R' and resid 247 through 260 removed outlier: 3.546A pdb=" N HIS R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 301 removed outlier: 4.963A pdb=" N CYS R 291 " --> pdb=" O MET R 287 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS R 292 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.527A pdb=" N TYR R 298 " --> pdb=" O ASP R 294 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE R 300 " --> pdb=" O PHE R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 310 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.610A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 63 removed outlier: 3.570A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63 removed outlier: 3.570A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.798A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.798A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.908A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 223 " --> pdb=" O CYS H 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.843A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR K 80 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.187A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 Processing sheet with id=AB4, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.435A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.556A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 147 through 152 360 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.71 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: 2242 1.34 - 1.46: 1464 1.46 - 1.58: 3557 1.58 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 7315 Sorted by residual: bond pdb=" C17 KKF R1301 " pdb=" N07 KKF R1301 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C22 KKF R1301 " pdb=" C26 KKF R1301 " ideal model delta sigma weight residual 1.460 1.524 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C13 KKF R1301 " pdb=" N07 KKF R1301 " ideal model delta sigma weight residual 1.459 1.514 -0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" C15 KKF R1301 " pdb=" O05 KKF R1301 " ideal model delta sigma weight residual 1.207 1.257 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C16 KKF R1301 " pdb=" N08 KKF R1301 " ideal model delta sigma weight residual 1.438 1.487 -0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 7310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 9691 2.41 - 4.82: 198 4.82 - 7.23: 41 7.23 - 9.65: 7 9.65 - 12.06: 2 Bond angle restraints: 9939 Sorted by residual: angle pdb=" N VAL R 206 " pdb=" CA VAL R 206 " pdb=" C VAL R 206 " ideal model delta sigma weight residual 110.42 117.64 -7.22 9.60e-01 1.09e+00 5.65e+01 angle pdb=" C GLU R 183 " pdb=" N TYR R 184 " pdb=" CA TYR R 184 " ideal model delta sigma weight residual 120.44 126.13 -5.69 1.30e+00 5.92e-01 1.91e+01 angle pdb=" N TYR R 205 " pdb=" CA TYR R 205 " pdb=" C TYR R 205 " ideal model delta sigma weight residual 112.72 118.18 -5.46 1.28e+00 6.10e-01 1.82e+01 angle pdb=" CA LEU R 207 " pdb=" C LEU R 207 " pdb=" N PRO R 208 " ideal model delta sigma weight residual 120.93 116.62 4.31 1.06e+00 8.90e-01 1.65e+01 angle pdb=" C17 KKF R1301 " pdb=" C19 KKF R1301 " pdb=" C22 KKF R1301 " ideal model delta sigma weight residual 120.00 132.06 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 9934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4009 17.80 - 35.59: 296 35.59 - 53.39: 45 53.39 - 71.19: 4 71.19 - 88.99: 6 Dihedral angle restraints: 4360 sinusoidal: 1657 harmonic: 2703 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 28.93 64.07 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 138.60 -45.60 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CA GLU K 44 " pdb=" C GLU K 44 " pdb=" N ARG K 45 " pdb=" CA ARG K 45 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 724 0.041 - 0.082: 286 0.082 - 0.122: 102 0.122 - 0.163: 15 0.163 - 0.204: 8 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA TYR R 205 " pdb=" N TYR R 205 " pdb=" C TYR R 205 " pdb=" CB TYR R 205 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE R 210 " pdb=" N ILE R 210 " pdb=" C ILE R 210 " pdb=" CB ILE R 210 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR L 142 " pdb=" N TYR L 142 " pdb=" C TYR L 142 " pdb=" CB TYR L 142 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1132 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO H 109 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 294 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO R 295 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 295 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 295 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 164 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO R 165 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.029 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 695 2.74 - 3.28: 7168 3.28 - 3.82: 11624 3.82 - 4.36: 13933 4.36 - 4.90: 23820 Nonbonded interactions: 57240 Sorted by model distance: nonbonded pdb=" OH TYR R 38 " pdb=" OD1 ASN R 288 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLU L 107 " pdb=" OH TYR L 175 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR R 205 " pdb=" OG1 THR R 248 " model vdw 2.295 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" OD2 ASP H 93 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU K 6 " pdb=" N GLY K 114 " model vdw 2.307 3.120 ... (remaining 57235 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.005 0.073 7321 Z= 0.237 Angle : 0.869 12.057 9951 Z= 0.452 Chirality : 0.051 0.204 1135 Planarity : 0.006 0.058 1250 Dihedral : 12.817 88.986 2600 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.26 % Allowed : 3.24 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.24), residues: 904 helix: -1.93 (0.24), residues: 316 sheet: -2.09 (0.31), residues: 238 loop : -3.08 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R1039 TYR 0.018 0.001 TYR H 53 PHE 0.013 0.002 PHE H 114 TRP 0.011 0.002 TRP H 50 HIS 0.008 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7315) covalent geometry : angle 0.86848 ( 9939) SS BOND : bond 0.00396 ( 6) SS BOND : angle 1.01102 ( 12) hydrogen bonds : bond 0.17095 ( 344) hydrogen bonds : angle 7.63128 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7819 (t0) cc_final: 0.7487 (t0) REVERT: H 92 GLU cc_start: 0.8639 (pm20) cc_final: 0.8316 (pm20) REVERT: H 185 GLN cc_start: 0.8579 (tt0) cc_final: 0.8193 (mt0) REVERT: H 209 ILE cc_start: 0.8768 (pt) cc_final: 0.8443 (pp) REVERT: H 226 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8478 (mt-10) REVERT: K 30 SER cc_start: 0.8593 (p) cc_final: 0.8287 (m) REVERT: K 34 MET cc_start: 0.7706 (mmt) cc_final: 0.7474 (mmt) REVERT: K 46 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7350 (mp0) REVERT: K 98 ILE cc_start: 0.8458 (tp) cc_final: 0.8038 (tp) REVERT: K 101 ASP cc_start: 0.8695 (t0) cc_final: 0.8341 (t0) REVERT: L 124 ASP cc_start: 0.9072 (p0) cc_final: 0.8817 (m-30) REVERT: L 128 LYS cc_start: 0.9215 (mptt) cc_final: 0.9007 (mmtm) REVERT: L 167 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8083 (tp30) REVERT: L 192 LYS cc_start: 0.8498 (pttp) cc_final: 0.8170 (mmtt) REVERT: R 37 HIS cc_start: 0.7186 (t70) cc_final: 0.6812 (t-170) REVERT: R 156 TRP cc_start: 0.8127 (t-100) cc_final: 0.7870 (m100) REVERT: R 202 PHE cc_start: 0.7816 (t80) cc_final: 0.7366 (m-80) REVERT: R 1091 GLU cc_start: 0.8037 (mp0) cc_final: 0.7706 (mp0) REVERT: R 288 ASN cc_start: 0.7678 (m110) cc_final: 0.7224 (m110) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.5116 time to fit residues: 79.4770 Evaluate side-chains 105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN L 126 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1030 GLN R1104 ASN R1108 GLN R 234 ASN R 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086794 restraints weight = 12992.172| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.27 r_work: 0.3155 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 7321 Z= 0.278 Angle : 0.768 12.449 9951 Z= 0.393 Chirality : 0.048 0.172 1135 Planarity : 0.005 0.047 1250 Dihedral : 6.140 55.345 1030 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.72 % Allowed : 14.38 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.26), residues: 904 helix: -0.88 (0.27), residues: 317 sheet: -1.95 (0.30), residues: 252 loop : -2.65 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 31 TYR 0.025 0.002 TYR R 298 PHE 0.013 0.002 PHE R 296 TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS R 281 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 7315) covalent geometry : angle 0.76701 ( 9939) SS BOND : bond 0.00379 ( 6) SS BOND : angle 1.19683 ( 12) hydrogen bonds : bond 0.04396 ( 344) hydrogen bonds : angle 5.58393 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8066 (t0) cc_final: 0.7497 (OUTLIER) REVERT: H 79 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8515 (mttm) REVERT: H 92 GLU cc_start: 0.8884 (pm20) cc_final: 0.8583 (pm20) REVERT: H 185 GLN cc_start: 0.8856 (tt0) cc_final: 0.8537 (mt0) REVERT: H 209 ILE cc_start: 0.8698 (pt) cc_final: 0.8422 (pp) REVERT: H 226 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8415 (mt-10) REVERT: K 19 ARG cc_start: 0.8422 (ttt90) cc_final: 0.8212 (ttm170) REVERT: K 34 MET cc_start: 0.8237 (mmt) cc_final: 0.7965 (mmt) REVERT: K 46 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7824 (mp0) REVERT: K 87 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7934 (mtmm) REVERT: K 98 ILE cc_start: 0.8729 (tp) cc_final: 0.8353 (tp) REVERT: K 101 ASP cc_start: 0.8753 (t0) cc_final: 0.8297 (t0) REVERT: L 128 LYS cc_start: 0.9236 (mptt) cc_final: 0.8932 (mmtm) REVERT: L 192 LYS cc_start: 0.8718 (pttp) cc_final: 0.8185 (mmtt) REVERT: R 34 MET cc_start: 0.3754 (ttt) cc_final: 0.3257 (ttt) REVERT: R 202 PHE cc_start: 0.8110 (t80) cc_final: 0.7449 (m-10) REVERT: R 1009 GLU cc_start: 0.8920 (tp30) cc_final: 0.8679 (tp30) REVERT: R 1091 GLU cc_start: 0.8397 (mp0) cc_final: 0.7969 (mp0) REVERT: R 288 ASN cc_start: 0.8219 (m110) cc_final: 0.7495 (m110) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 0.5082 time to fit residues: 65.1417 Evaluate side-chains 107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 HIS R 147 HIS R 234 ASN R 281 HIS R 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.133300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088107 restraints weight = 12894.466| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.27 r_work: 0.3187 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7321 Z= 0.201 Angle : 0.707 11.500 9951 Z= 0.359 Chirality : 0.045 0.153 1135 Planarity : 0.005 0.048 1250 Dihedral : 5.847 54.711 1030 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.15 % Allowed : 15.54 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.26), residues: 904 helix: -0.42 (0.28), residues: 305 sheet: -1.74 (0.30), residues: 259 loop : -2.32 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 31 TYR 0.018 0.001 TYR L 142 PHE 0.011 0.001 PHE R 296 TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS R 281 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7315) covalent geometry : angle 0.70579 ( 9939) SS BOND : bond 0.00393 ( 6) SS BOND : angle 1.19933 ( 12) hydrogen bonds : bond 0.03883 ( 344) hydrogen bonds : angle 5.25195 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8003 (t0) cc_final: 0.7363 (t0) REVERT: H 79 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8451 (mttm) REVERT: H 92 GLU cc_start: 0.8900 (pm20) cc_final: 0.8554 (pm20) REVERT: H 185 GLN cc_start: 0.8827 (tt0) cc_final: 0.8519 (mt0) REVERT: H 209 ILE cc_start: 0.8770 (pt) cc_final: 0.8500 (pp) REVERT: H 226 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8388 (mt-10) REVERT: K 31 ARG cc_start: 0.8346 (ptm160) cc_final: 0.7872 (ttp-170) REVERT: K 46 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7798 (mp0) REVERT: K 87 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7911 (mtmm) REVERT: K 101 ASP cc_start: 0.8749 (t0) cc_final: 0.8267 (t0) REVERT: L 192 LYS cc_start: 0.8354 (pttp) cc_final: 0.8043 (mmtt) REVERT: R 34 MET cc_start: 0.4070 (ttt) cc_final: 0.3433 (ttt) REVERT: R 156 TRP cc_start: 0.8173 (t-100) cc_final: 0.7906 (m100) REVERT: R 202 PHE cc_start: 0.8148 (t80) cc_final: 0.7488 (m-10) REVERT: R 1013 GLU cc_start: 0.8704 (tp30) cc_final: 0.8492 (tt0) REVERT: R 1091 GLU cc_start: 0.8389 (mp0) cc_final: 0.7931 (mp0) REVERT: R 288 ASN cc_start: 0.8351 (m-40) cc_final: 0.7586 (m110) outliers start: 32 outliers final: 11 residues processed: 123 average time/residue: 0.4386 time to fit residues: 57.3848 Evaluate side-chains 103 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 91 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 HIS ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1018 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089388 restraints weight = 12926.434| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.38 r_work: 0.3236 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7321 Z= 0.128 Angle : 0.663 10.972 9951 Z= 0.332 Chirality : 0.044 0.164 1135 Planarity : 0.004 0.050 1250 Dihedral : 5.374 50.856 1030 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.11 % Allowed : 18.65 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.27), residues: 904 helix: 0.02 (0.29), residues: 303 sheet: -1.40 (0.31), residues: 257 loop : -2.05 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 31 TYR 0.013 0.001 TYR R 298 PHE 0.009 0.001 PHE L 141 TRP 0.015 0.001 TRP K 111 HIS 0.006 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7315) covalent geometry : angle 0.66222 ( 9939) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.05180 ( 12) hydrogen bonds : bond 0.03311 ( 344) hydrogen bonds : angle 4.84613 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7956 (t0) cc_final: 0.7253 (t0) REVERT: H 79 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8474 (mtpt) REVERT: H 92 GLU cc_start: 0.8859 (pm20) cc_final: 0.8503 (pm20) REVERT: H 185 GLN cc_start: 0.8794 (tt0) cc_final: 0.8485 (mt0) REVERT: H 209 ILE cc_start: 0.8801 (pt) cc_final: 0.8539 (pp) REVERT: H 226 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8396 (mt-10) REVERT: K 31 ARG cc_start: 0.8383 (ptm160) cc_final: 0.7955 (ttp-170) REVERT: K 46 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7771 (mp0) REVERT: K 87 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7870 (mtmm) REVERT: K 101 ASP cc_start: 0.8750 (t0) cc_final: 0.8113 (t0) REVERT: L 107 GLU cc_start: 0.8367 (pt0) cc_final: 0.7891 (pt0) REVERT: L 192 LYS cc_start: 0.8506 (pttp) cc_final: 0.8231 (pttt) REVERT: R 34 MET cc_start: 0.3743 (ttt) cc_final: 0.3388 (ttt) REVERT: R 156 TRP cc_start: 0.8152 (t-100) cc_final: 0.7849 (m100) REVERT: R 198 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6204 (tp) REVERT: R 202 PHE cc_start: 0.8097 (t80) cc_final: 0.7473 (m-10) REVERT: R 1091 GLU cc_start: 0.8355 (mp0) cc_final: 0.7819 (mp0) REVERT: R 285 CYS cc_start: 0.8285 (m) cc_final: 0.7652 (m) REVERT: R 288 ASN cc_start: 0.8289 (m-40) cc_final: 0.7206 (t0) outliers start: 24 outliers final: 8 residues processed: 122 average time/residue: 0.4177 time to fit residues: 54.4800 Evaluate side-chains 101 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 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 = 0.4025 r_free = 0.4025 target = 0.135428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089026 restraints weight = 12769.240| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.37 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7321 Z= 0.140 Angle : 0.673 10.234 9951 Z= 0.338 Chirality : 0.044 0.147 1135 Planarity : 0.004 0.050 1250 Dihedral : 5.366 53.072 1030 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.76 % Allowed : 19.56 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.28), residues: 904 helix: 0.10 (0.29), residues: 311 sheet: -1.20 (0.32), residues: 242 loop : -1.81 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.015 0.001 TYR L 142 PHE 0.009 0.001 PHE L 141 TRP 0.016 0.001 TRP K 111 HIS 0.002 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7315) covalent geometry : angle 0.67228 ( 9939) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.93084 ( 12) hydrogen bonds : bond 0.03306 ( 344) hydrogen bonds : angle 4.70370 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8001 (t0) cc_final: 0.7283 (t0) REVERT: H 79 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: H 92 GLU cc_start: 0.8866 (pm20) cc_final: 0.8507 (pm20) REVERT: H 185 GLN cc_start: 0.8775 (tt0) cc_final: 0.8472 (mt0) REVERT: H 209 ILE cc_start: 0.8841 (pt) cc_final: 0.8580 (pp) REVERT: H 226 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8415 (mt-10) REVERT: K 18 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7070 (mp) REVERT: K 46 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7777 (mp0) REVERT: K 87 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7519 (mmtm) REVERT: K 101 ASP cc_start: 0.8760 (t0) cc_final: 0.8146 (t0) REVERT: L 107 GLU cc_start: 0.8351 (pt0) cc_final: 0.8012 (pt0) REVERT: R 34 MET cc_start: 0.3850 (ttt) cc_final: 0.3186 (ttt) REVERT: R 156 TRP cc_start: 0.8142 (t-100) cc_final: 0.7921 (m100) REVERT: R 162 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: R 202 PHE cc_start: 0.8096 (t80) cc_final: 0.7499 (m-10) REVERT: R 1091 GLU cc_start: 0.8384 (mp0) cc_final: 0.7845 (mp0) REVERT: R 243 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5817 (t80) REVERT: R 285 CYS cc_start: 0.8301 (m) cc_final: 0.7705 (m) REVERT: R 288 ASN cc_start: 0.8162 (m-40) cc_final: 0.7355 (m110) outliers start: 29 outliers final: 9 residues processed: 114 average time/residue: 0.4302 time to fit residues: 52.2259 Evaluate side-chains 101 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.133898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087660 restraints weight = 12894.022| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.38 r_work: 0.3209 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7321 Z= 0.170 Angle : 0.701 12.339 9951 Z= 0.351 Chirality : 0.044 0.177 1135 Planarity : 0.004 0.055 1250 Dihedral : 5.447 56.283 1030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.76 % Allowed : 20.08 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.28), residues: 904 helix: 0.10 (0.29), residues: 311 sheet: -1.11 (0.32), residues: 242 loop : -1.69 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 31 TYR 0.020 0.001 TYR R 69 PHE 0.009 0.001 PHE R 289 TRP 0.015 0.001 TRP K 111 HIS 0.002 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7315) covalent geometry : angle 0.70064 ( 9939) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.02030 ( 12) hydrogen bonds : bond 0.03433 ( 344) hydrogen bonds : angle 4.69197 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7955 (t0) cc_final: 0.7231 (t0) REVERT: H 79 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8467 (mtpt) REVERT: H 92 GLU cc_start: 0.8868 (pm20) cc_final: 0.8501 (pm20) REVERT: H 185 GLN cc_start: 0.8755 (tt0) cc_final: 0.8445 (mt0) REVERT: H 209 ILE cc_start: 0.8815 (pt) cc_final: 0.8540 (pp) REVERT: H 226 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8389 (mt-10) REVERT: K 18 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7189 (mp) REVERT: K 31 ARG cc_start: 0.8403 (ptm160) cc_final: 0.7841 (ttp-170) REVERT: K 46 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7752 (mp0) REVERT: K 87 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7565 (mmtm) REVERT: K 101 ASP cc_start: 0.8743 (t0) cc_final: 0.8093 (t0) REVERT: L 107 GLU cc_start: 0.8277 (pt0) cc_final: 0.7960 (pt0) REVERT: R 34 MET cc_start: 0.3966 (ttt) cc_final: 0.3361 (ttt) REVERT: R 162 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: R 202 PHE cc_start: 0.8111 (t80) cc_final: 0.7514 (m-10) REVERT: R 1091 GLU cc_start: 0.8386 (mp0) cc_final: 0.7838 (mp0) REVERT: R 285 CYS cc_start: 0.8307 (m) cc_final: 0.7703 (m) REVERT: R 288 ASN cc_start: 0.8102 (m-40) cc_final: 0.7267 (m110) outliers start: 29 outliers final: 12 residues processed: 114 average time/residue: 0.4721 time to fit residues: 57.3090 Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087122 restraints weight = 12961.498| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.38 r_work: 0.3197 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7321 Z= 0.188 Angle : 0.713 11.025 9951 Z= 0.359 Chirality : 0.045 0.172 1135 Planarity : 0.004 0.056 1250 Dihedral : 5.530 56.884 1030 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.11 % Allowed : 22.28 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.28), residues: 904 helix: 0.12 (0.29), residues: 311 sheet: -1.05 (0.32), residues: 242 loop : -1.60 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 31 TYR 0.032 0.001 TYR R 69 PHE 0.009 0.001 PHE L 100 TRP 0.015 0.001 TRP K 111 HIS 0.003 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7315) covalent geometry : angle 0.71224 ( 9939) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.12339 ( 12) hydrogen bonds : bond 0.03472 ( 344) hydrogen bonds : angle 4.71029 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7990 (t0) cc_final: 0.7233 (t0) REVERT: H 79 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8444 (mtpt) REVERT: H 92 GLU cc_start: 0.8887 (pm20) cc_final: 0.8522 (pm20) REVERT: H 185 GLN cc_start: 0.8744 (tt0) cc_final: 0.8488 (mt0) REVERT: H 209 ILE cc_start: 0.8845 (pt) cc_final: 0.8573 (pp) REVERT: H 226 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8366 (mt-10) REVERT: K 18 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7267 (mp) REVERT: K 31 ARG cc_start: 0.8375 (ptm160) cc_final: 0.7853 (ttp-170) REVERT: K 46 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7759 (mp0) REVERT: K 87 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7550 (mmtm) REVERT: K 101 ASP cc_start: 0.8736 (t0) cc_final: 0.8090 (t0) REVERT: L 107 GLU cc_start: 0.8300 (pt0) cc_final: 0.7953 (pt0) REVERT: R 34 MET cc_start: 0.4040 (ttt) cc_final: 0.3455 (ttt) REVERT: R 202 PHE cc_start: 0.8108 (t80) cc_final: 0.7519 (m-10) REVERT: R 1091 GLU cc_start: 0.8402 (mp0) cc_final: 0.7863 (mp0) REVERT: R 243 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.5574 (t80) REVERT: R 288 ASN cc_start: 0.8126 (m-40) cc_final: 0.7280 (m110) outliers start: 24 outliers final: 13 residues processed: 109 average time/residue: 0.4410 time to fit residues: 51.3035 Evaluate side-chains 103 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1013 GLU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.133952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087420 restraints weight = 13047.515| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.40 r_work: 0.3200 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7321 Z= 0.180 Angle : 0.713 10.537 9951 Z= 0.357 Chirality : 0.045 0.179 1135 Planarity : 0.004 0.056 1250 Dihedral : 5.498 56.468 1030 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.11 % Allowed : 22.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 904 helix: 0.20 (0.29), residues: 311 sheet: -1.01 (0.32), residues: 248 loop : -1.52 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 31 TYR 0.016 0.001 TYR L 142 PHE 0.010 0.001 PHE R 289 TRP 0.017 0.001 TRP K 111 HIS 0.002 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7315) covalent geometry : angle 0.71278 ( 9939) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.08778 ( 12) hydrogen bonds : bond 0.03346 ( 344) hydrogen bonds : angle 4.67199 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8355 (tt0) cc_final: 0.8103 (pt0) REVERT: H 76 ASP cc_start: 0.8017 (t0) cc_final: 0.7255 (t0) REVERT: H 79 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8464 (mtpt) REVERT: H 92 GLU cc_start: 0.8894 (pm20) cc_final: 0.8536 (pm20) REVERT: H 185 GLN cc_start: 0.8736 (tt0) cc_final: 0.8489 (mt0) REVERT: H 209 ILE cc_start: 0.8794 (pt) cc_final: 0.8509 (pp) REVERT: H 226 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8356 (mt-10) REVERT: K 18 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7315 (mp) REVERT: K 31 ARG cc_start: 0.8425 (ptm160) cc_final: 0.7904 (ttp-170) REVERT: K 46 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7820 (mp0) REVERT: K 87 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7549 (mmtm) REVERT: K 101 ASP cc_start: 0.8713 (t0) cc_final: 0.8030 (t0) REVERT: L 107 GLU cc_start: 0.8296 (pt0) cc_final: 0.7946 (pt0) REVERT: R 34 MET cc_start: 0.4015 (ttt) cc_final: 0.3594 (ttt) REVERT: R 162 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: R 202 PHE cc_start: 0.8155 (t80) cc_final: 0.7536 (m-10) REVERT: R 1091 GLU cc_start: 0.8415 (mp0) cc_final: 0.7887 (mp0) REVERT: R 243 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.5988 (t80) REVERT: R 285 CYS cc_start: 0.8322 (m) cc_final: 0.7672 (m) REVERT: R 288 ASN cc_start: 0.8077 (m-40) cc_final: 0.7120 (m110) outliers start: 24 outliers final: 15 residues processed: 108 average time/residue: 0.4852 time to fit residues: 55.6585 Evaluate side-chains 108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1013 GLU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 HIS R 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086297 restraints weight = 12893.790| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.38 r_work: 0.3182 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7321 Z= 0.205 Angle : 0.744 14.376 9951 Z= 0.372 Chirality : 0.046 0.183 1135 Planarity : 0.004 0.054 1250 Dihedral : 5.576 56.032 1030 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.37 % Allowed : 23.06 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.28), residues: 904 helix: 0.18 (0.29), residues: 311 sheet: -0.95 (0.33), residues: 238 loop : -1.51 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 31 TYR 0.018 0.001 TYR L 142 PHE 0.009 0.001 PHE L 100 TRP 0.017 0.001 TRP K 111 HIS 0.003 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 7315) covalent geometry : angle 0.74351 ( 9939) SS BOND : bond 0.00268 ( 6) SS BOND : angle 1.12417 ( 12) hydrogen bonds : bond 0.03569 ( 344) hydrogen bonds : angle 4.74522 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.273 Fit side-chains REVERT: H 6 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: H 76 ASP cc_start: 0.7980 (t0) cc_final: 0.7210 (t0) REVERT: H 79 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: H 92 GLU cc_start: 0.8897 (pm20) cc_final: 0.8540 (pm20) REVERT: H 185 GLN cc_start: 0.8722 (tt0) cc_final: 0.8434 (mt0) REVERT: H 209 ILE cc_start: 0.8738 (pt) cc_final: 0.8440 (pp) REVERT: H 226 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8384 (mt-10) REVERT: K 18 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7324 (mp) REVERT: K 31 ARG cc_start: 0.8460 (ptm160) cc_final: 0.7939 (ttp-170) REVERT: K 46 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7775 (mp0) REVERT: K 87 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7556 (mmtm) REVERT: K 101 ASP cc_start: 0.8718 (t0) cc_final: 0.8031 (t0) REVERT: L 107 GLU cc_start: 0.8315 (pt0) cc_final: 0.7951 (pt0) REVERT: R 34 MET cc_start: 0.4177 (ttt) cc_final: 0.3765 (ttt) REVERT: R 162 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: R 202 PHE cc_start: 0.8180 (t80) cc_final: 0.7521 (m-10) REVERT: R 1091 GLU cc_start: 0.8416 (mp0) cc_final: 0.7884 (mp0) REVERT: R 243 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.5743 (t80) REVERT: R 285 CYS cc_start: 0.8337 (m) cc_final: 0.7713 (m) REVERT: R 288 ASN cc_start: 0.8300 (m-40) cc_final: 0.7420 (m110) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.4852 time to fit residues: 57.2072 Evaluate side-chains 105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.0270 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 HIS R 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.133797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088660 restraints weight = 12923.054| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.29 r_work: 0.3194 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7321 Z= 0.195 Angle : 0.764 16.804 9951 Z= 0.381 Chirality : 0.046 0.212 1135 Planarity : 0.005 0.057 1250 Dihedral : 5.704 49.449 1030 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 23.83 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.28), residues: 904 helix: 0.17 (0.29), residues: 310 sheet: -0.89 (0.33), residues: 240 loop : -1.48 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 31 TYR 0.016 0.001 TYR L 142 PHE 0.009 0.001 PHE R 289 TRP 0.016 0.001 TRP K 111 HIS 0.002 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7315) covalent geometry : angle 0.76350 ( 9939) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.03721 ( 12) hydrogen bonds : bond 0.03612 ( 344) hydrogen bonds : angle 4.77051 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.293 Fit side-chains REVERT: H 6 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: H 76 ASP cc_start: 0.7996 (t0) cc_final: 0.7229 (t0) REVERT: H 79 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8412 (mtpt) REVERT: H 92 GLU cc_start: 0.8897 (pm20) cc_final: 0.8522 (pm20) REVERT: H 185 GLN cc_start: 0.8722 (tt0) cc_final: 0.8451 (mt0) REVERT: H 209 ILE cc_start: 0.8775 (pt) cc_final: 0.8484 (pp) REVERT: H 226 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8384 (mt-10) REVERT: K 18 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7353 (mp) REVERT: K 34 MET cc_start: 0.8155 (mmp) cc_final: 0.7907 (mmp) REVERT: K 46 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7812 (mp0) REVERT: K 87 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7566 (mmtm) REVERT: K 98 ILE cc_start: 0.8393 (tp) cc_final: 0.8050 (mt) REVERT: K 101 ASP cc_start: 0.8727 (t0) cc_final: 0.8036 (t0) REVERT: L 107 GLU cc_start: 0.8322 (pt0) cc_final: 0.7955 (pt0) REVERT: R 146 GLU cc_start: 0.7281 (pp20) cc_final: 0.5587 (mm-30) REVERT: R 162 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: R 202 PHE cc_start: 0.8137 (t80) cc_final: 0.7507 (m-10) REVERT: R 1013 GLU cc_start: 0.8696 (tt0) cc_final: 0.8263 (tp30) REVERT: R 1091 GLU cc_start: 0.8416 (mp0) cc_final: 0.7892 (mp0) REVERT: R 243 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.5814 (t80) REVERT: R 285 CYS cc_start: 0.8342 (m) cc_final: 0.7738 (m) REVERT: R 288 ASN cc_start: 0.8274 (m-40) cc_final: 0.7332 (m110) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 0.4689 time to fit residues: 53.3816 Evaluate side-chains 109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 0.0070 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 overall best weight: 0.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 162 GLN R 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.137065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.091409 restraints weight = 12710.334| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.46 r_work: 0.3231 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7321 Z= 0.124 Angle : 0.741 17.149 9951 Z= 0.365 Chirality : 0.044 0.202 1135 Planarity : 0.005 0.063 1250 Dihedral : 5.206 50.771 1030 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.72 % Allowed : 23.83 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.29), residues: 904 helix: 0.34 (0.30), residues: 315 sheet: -0.64 (0.34), residues: 229 loop : -1.28 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 31 TYR 0.022 0.001 TYR R 69 PHE 0.010 0.001 PHE L 141 TRP 0.020 0.001 TRP K 111 HIS 0.004 0.001 HIS R 281 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7315) covalent geometry : angle 0.74116 ( 9939) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.77475 ( 12) hydrogen bonds : bond 0.03341 ( 344) hydrogen bonds : angle 4.51128 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.78 seconds wall clock time: 43 minutes 21.43 seconds (2601.43 seconds total)