Starting phenix.real_space_refine on Wed Mar 12 05:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_26135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_26135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_26135.map" model { file = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_26135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tuy_26135/03_2025/7tuy_26135.cif" } resolution = 2.98 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= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP: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: 5.79, per 1000 atoms: 0.81 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: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 2.12 Time building geometry restraints manager: 2.22 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: 96.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.040 ------------------------------------------------------------------------------- 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 7315 Z= 0.330 Angle : 0.868 12.057 9939 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 : 7.13 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 (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: -3.71 (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 TRP 0.011 0.002 TRP H 50 HIS 0.008 0.001 HIS R 251 PHE 0.013 0.002 PHE H 114 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG R1039 *********************** 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 : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7819 (t0) cc_final: 0.7489 (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: 0.7419 (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: 0.8052 (tp) REVERT: K 101 ASP cc_start: 0.8694 (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: 0.7871 (m100) REVERT: R 202 PHE cc_start: 0.7816 (t80) cc_final: 0.7364 (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: 0.7220 (m110) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 1.3902 time to fit residues: 215.9511 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 : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.136835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.091533 restraints weight = 12802.149| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.33 r_work: 0.3268 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7315 Z= 0.176 Angle : 0.666 12.628 9939 Z= 0.337 Chirality : 0.044 0.194 1135 Planarity : 0.005 0.047 1250 Dihedral : 5.619 52.441 1030 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.33 % Allowed : 12.18 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 904 helix: -0.64 (0.27), residues: 314 sheet: -1.84 (0.30), residues: 251 loop : -2.49 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 111 HIS 0.006 0.001 HIS R 281 PHE 0.008 0.001 PHE R 289 TYR 0.025 0.001 TYR R 298 ARG 0.007 0.000 ARG K 31 *********************** 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 135 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8045 (t0) cc_final: 0.7469 (OUTLIER) REVERT: H 79 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8552 (mtpt) REVERT: H 92 GLU cc_start: 0.8840 (pm20) cc_final: 0.8525 (pm20) REVERT: H 119 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8702 (pt0) REVERT: H 185 GLN cc_start: 0.8864 (tt0) cc_final: 0.8569 (mt0) REVERT: H 209 ILE cc_start: 0.8759 (pt) cc_final: 0.8496 (pp) REVERT: H 226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8533 (mt-10) REVERT: K 31 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7920 (ttp-170) REVERT: K 34 MET cc_start: 0.8229 (mmt) cc_final: 0.7979 (mmt) REVERT: K 46 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7780 (mp0) REVERT: K 74 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: K 87 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7836 (mtmm) REVERT: K 98 ILE cc_start: 0.8624 (tp) cc_final: 0.8321 (tp) REVERT: K 101 ASP cc_start: 0.8755 (t0) cc_final: 0.8230 (t0) REVERT: L 107 GLU cc_start: 0.8423 (pt0) cc_final: 0.7888 (pt0) REVERT: L 124 ASP cc_start: 0.9069 (p0) cc_final: 0.8845 (OUTLIER) REVERT: L 128 LYS cc_start: 0.9229 (mptt) cc_final: 0.8952 (mmtm) REVERT: L 192 LYS cc_start: 0.8668 (pttp) cc_final: 0.8276 (mmtt) REVERT: L 213 ARG cc_start: 0.7112 (tpt90) cc_final: 0.6845 (tpt90) REVERT: R 34 MET cc_start: 0.3458 (ttt) cc_final: 0.3213 (ttt) REVERT: R 198 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6113 (mt) REVERT: R 202 PHE cc_start: 0.7983 (t80) cc_final: 0.7355 (m-10) REVERT: R 1091 GLU cc_start: 0.8261 (mp0) cc_final: 0.7816 (mp0) REVERT: R 288 ASN cc_start: 0.8107 (m110) cc_final: 0.7238 (m110) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 1.1598 time to fit residues: 154.5834 Evaluate side-chains 113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain K residue 74 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** R1018 ASN R 234 ASN R 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.135587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089419 restraints weight = 13028.765| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.37 r_work: 0.3233 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7315 Z= 0.226 Angle : 0.667 9.234 9939 Z= 0.337 Chirality : 0.044 0.160 1135 Planarity : 0.004 0.047 1250 Dihedral : 5.513 54.673 1030 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.72 % Allowed : 15.80 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.27), residues: 904 helix: -0.24 (0.28), residues: 313 sheet: -1.58 (0.31), residues: 251 loop : -2.21 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 111 HIS 0.003 0.001 HIS R 281 PHE 0.007 0.001 PHE L 141 TYR 0.018 0.001 TYR R 69 ARG 0.004 0.000 ARG H 90 *********************** 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 127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8001 (t0) cc_final: 0.7335 (t0) REVERT: H 79 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8478 (mtpt) REVERT: H 92 GLU cc_start: 0.8865 (pm20) cc_final: 0.8525 (pm20) REVERT: H 119 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: H 185 GLN cc_start: 0.8833 (tt0) cc_final: 0.8544 (mt0) REVERT: H 209 ILE cc_start: 0.8768 (pt) cc_final: 0.8504 (pp) REVERT: H 226 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8479 (mt-10) REVERT: K 31 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8069 (ttm170) REVERT: K 46 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7753 (mp0) REVERT: K 87 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7874 (mtmm) REVERT: K 101 ASP cc_start: 0.8763 (t0) cc_final: 0.8162 (t0) REVERT: L 107 GLU cc_start: 0.8451 (pt0) cc_final: 0.7957 (pt0) REVERT: L 124 ASP cc_start: 0.9097 (p0) cc_final: 0.8807 (m-30) REVERT: L 128 LYS cc_start: 0.9235 (mptt) cc_final: 0.9003 (mmtm) REVERT: L 192 LYS cc_start: 0.8423 (pttp) cc_final: 0.8140 (mmtt) REVERT: R 34 MET cc_start: 0.3921 (ttt) cc_final: 0.3215 (ttt) REVERT: R 156 TRP cc_start: 0.8187 (t-100) cc_final: 0.7919 (m100) REVERT: R 198 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6098 (mt) REVERT: R 202 PHE cc_start: 0.8027 (t80) cc_final: 0.7412 (m-10) REVERT: R 1091 GLU cc_start: 0.8335 (mp0) cc_final: 0.7851 (mp0) REVERT: R 287 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7755 (ttm) REVERT: R 288 ASN cc_start: 0.8139 (m-40) cc_final: 0.7495 (m110) REVERT: R 294 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.7007 (t70) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 1.0826 time to fit residues: 135.6970 Evaluate side-chains 109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 119 GLN 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 R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Chi-restraints excluded: chain R residue 294 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.132836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086026 restraints weight = 12908.674| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.37 r_work: 0.3178 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7315 Z= 0.357 Angle : 0.710 8.679 9939 Z= 0.363 Chirality : 0.046 0.161 1135 Planarity : 0.004 0.050 1250 Dihedral : 5.648 54.903 1030 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.63 % Allowed : 17.49 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.27), residues: 904 helix: -0.18 (0.29), residues: 314 sheet: -1.50 (0.31), residues: 256 loop : -2.02 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.006 0.001 HIS R 37 PHE 0.009 0.001 PHE R 296 TYR 0.019 0.002 TYR L 142 ARG 0.006 0.000 ARG L 213 *********************** 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 122 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8004 (t0) cc_final: 0.7304 (t0) REVERT: H 79 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: H 92 GLU cc_start: 0.8903 (pm20) cc_final: 0.8545 (pm20) REVERT: H 185 GLN cc_start: 0.8806 (tt0) cc_final: 0.8526 (mt0) REVERT: H 209 ILE cc_start: 0.8756 (pt) cc_final: 0.8484 (pp) REVERT: H 226 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8454 (mt-10) REVERT: K 46 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7772 (mp0) REVERT: K 74 ASP cc_start: 0.8197 (m-30) cc_final: 0.7969 (m-30) REVERT: K 87 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7845 (mtmm) REVERT: K 101 ASP cc_start: 0.8742 (t0) cc_final: 0.8253 (t0) REVERT: L 192 LYS cc_start: 0.8303 (pttp) cc_final: 0.8037 (mmtt) REVERT: R 34 MET cc_start: 0.3958 (ttt) cc_final: 0.3363 (ttt) REVERT: R 156 TRP cc_start: 0.8206 (t-100) cc_final: 0.7884 (m100) REVERT: R 198 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6030 (mt) REVERT: R 202 PHE cc_start: 0.8116 (t80) cc_final: 0.7492 (m-10) REVERT: R 1091 GLU cc_start: 0.8440 (mp0) cc_final: 0.7964 (mp0) REVERT: R 243 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.5872 (t80) REVERT: R 285 CYS cc_start: 0.8338 (m) cc_final: 0.7758 (m) REVERT: R 288 ASN cc_start: 0.8275 (m-40) cc_final: 0.7469 (m110) outliers start: 28 outliers final: 12 residues processed: 115 average time/residue: 0.9615 time to fit residues: 118.2477 Evaluate side-chains 106 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 62 ASP 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 R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 239 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.135694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089945 restraints weight = 12864.110| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.37 r_work: 0.3244 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7315 Z= 0.184 Angle : 0.653 10.263 9939 Z= 0.327 Chirality : 0.043 0.150 1135 Planarity : 0.004 0.056 1250 Dihedral : 5.250 51.903 1030 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.50 % Allowed : 18.65 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 904 helix: 0.10 (0.29), residues: 314 sheet: -1.17 (0.33), residues: 231 loop : -1.81 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 111 HIS 0.002 0.001 HIS R 281 PHE 0.008 0.001 PHE L 141 TYR 0.014 0.001 TYR R 69 ARG 0.009 0.000 ARG K 31 *********************** 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 132 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7940 (t0) cc_final: 0.7236 (t0) REVERT: H 79 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8498 (mtpt) REVERT: H 92 GLU cc_start: 0.8864 (pm20) cc_final: 0.8521 (pm20) REVERT: H 119 GLN cc_start: 0.9003 (pt0) cc_final: 0.8803 (pp30) REVERT: H 185 GLN cc_start: 0.8774 (tt0) cc_final: 0.8489 (mt0) REVERT: H 209 ILE cc_start: 0.8807 (pt) cc_final: 0.8527 (pp) REVERT: H 226 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8392 (mt-10) REVERT: K 31 ARG cc_start: 0.8420 (ptm160) cc_final: 0.7958 (ttp-170) REVERT: K 46 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7785 (mp0) REVERT: K 87 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7515 (mmtm) REVERT: K 101 ASP cc_start: 0.8718 (t0) cc_final: 0.8082 (t0) REVERT: L 107 GLU cc_start: 0.8458 (pt0) cc_final: 0.7930 (pt0) REVERT: L 192 LYS cc_start: 0.8320 (pttp) cc_final: 0.7978 (mmtt) REVERT: R 34 MET cc_start: 0.3758 (ttt) cc_final: 0.3475 (ttt) REVERT: R 198 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6123 (mt) REVERT: R 202 PHE cc_start: 0.8105 (t80) cc_final: 0.7519 (m-10) REVERT: R 1091 GLU cc_start: 0.8370 (mp0) cc_final: 0.7887 (mp0) REVERT: R 285 CYS cc_start: 0.8293 (m) cc_final: 0.7615 (m) REVERT: R 288 ASN cc_start: 0.8167 (m-40) cc_final: 0.7221 (m110) REVERT: R 294 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6903 (t70) outliers start: 27 outliers final: 8 residues processed: 124 average time/residue: 1.0312 time to fit residues: 136.2324 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 : 1.169 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 294 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.133342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086883 restraints weight = 12865.474| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.37 r_work: 0.3195 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7315 Z= 0.320 Angle : 0.705 9.379 9939 Z= 0.356 Chirality : 0.045 0.180 1135 Planarity : 0.004 0.053 1250 Dihedral : 5.427 52.239 1030 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.37 % Allowed : 19.56 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.28), residues: 904 helix: 0.11 (0.29), residues: 311 sheet: -1.14 (0.33), residues: 232 loop : -1.75 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 111 HIS 0.003 0.001 HIS H 214 PHE 0.009 0.001 PHE L 100 TYR 0.019 0.001 TYR L 142 ARG 0.007 0.000 ARG K 31 *********************** 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 118 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7985 (t0) cc_final: 0.7258 (t0) REVERT: H 79 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8451 (mtpt) REVERT: H 92 GLU cc_start: 0.8877 (pm20) cc_final: 0.8509 (pm20) REVERT: H 119 GLN cc_start: 0.9007 (pt0) cc_final: 0.8790 (pp30) REVERT: H 185 GLN cc_start: 0.8760 (tt0) cc_final: 0.8506 (mt0) REVERT: H 209 ILE cc_start: 0.8776 (pt) cc_final: 0.8515 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8429 (mt-10) REVERT: K 31 ARG cc_start: 0.8413 (ptm160) cc_final: 0.7926 (ttp-170) REVERT: K 46 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7780 (mp0) REVERT: K 87 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7565 (mmtm) REVERT: K 101 ASP cc_start: 0.8761 (t0) cc_final: 0.8152 (t0) REVERT: L 55 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9073 (tt) REVERT: L 107 GLU cc_start: 0.8453 (pt0) cc_final: 0.8013 (pt0) REVERT: L 192 LYS cc_start: 0.8319 (pttp) cc_final: 0.7928 (mmtm) REVERT: R 34 MET cc_start: 0.4100 (ttt) cc_final: 0.3477 (ttt) REVERT: R 198 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6139 (mt) REVERT: R 202 PHE cc_start: 0.8080 (t80) cc_final: 0.7499 (m-10) REVERT: R 1091 GLU cc_start: 0.8416 (mp0) cc_final: 0.7869 (mp0) REVERT: R 288 ASN cc_start: 0.8390 (m-40) cc_final: 0.7610 (m-40) outliers start: 26 outliers final: 15 residues processed: 111 average time/residue: 1.0714 time to fit residues: 126.5216 Evaluate side-chains 109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 L residue 12 LEU Chi-restraints excluded: chain L residue 55 LEU 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 L residue 199 THR Chi-restraints excluded: chain R residue 198 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 69 optimal weight: 0.0170 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.136748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091097 restraints weight = 12862.921| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.37 r_work: 0.3263 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7315 Z= 0.172 Angle : 0.657 9.687 9939 Z= 0.329 Chirality : 0.043 0.171 1135 Planarity : 0.004 0.057 1250 Dihedral : 5.016 46.399 1030 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.24 % Allowed : 19.69 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.29), residues: 904 helix: 0.27 (0.29), residues: 315 sheet: -0.97 (0.33), residues: 241 loop : -1.55 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 111 HIS 0.002 0.001 HIS H 214 PHE 0.009 0.001 PHE L 141 TYR 0.020 0.001 TYR R 69 ARG 0.006 0.000 ARG K 31 *********************** 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 133 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7994 (t0) cc_final: 0.7268 (t0) REVERT: H 79 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: H 92 GLU cc_start: 0.8847 (pm20) cc_final: 0.8521 (pm20) REVERT: H 119 GLN cc_start: 0.8952 (pt0) cc_final: 0.8740 (pp30) REVERT: H 185 GLN cc_start: 0.8749 (tt0) cc_final: 0.8487 (mt0) REVERT: H 209 ILE cc_start: 0.8812 (pt) cc_final: 0.8530 (pp) REVERT: H 226 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8457 (mt-10) REVERT: K 31 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8016 (ttp-170) REVERT: K 46 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7753 (mp0) REVERT: K 87 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7409 (mmtm) REVERT: K 101 ASP cc_start: 0.8704 (t0) cc_final: 0.8094 (t0) REVERT: L 55 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9027 (tt) REVERT: L 107 GLU cc_start: 0.8433 (pt0) cc_final: 0.7983 (pt0) REVERT: L 192 LYS cc_start: 0.8278 (pttp) cc_final: 0.7789 (mmtm) REVERT: R 34 MET cc_start: 0.3832 (ttt) cc_final: 0.3392 (ttt) REVERT: R 198 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6207 (mt) REVERT: R 202 PHE cc_start: 0.8060 (t80) cc_final: 0.7491 (m-10) REVERT: R 1091 GLU cc_start: 0.8339 (mp0) cc_final: 0.7777 (mp0) REVERT: R 243 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.5815 (t80) REVERT: R 284 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7370 (p) REVERT: R 285 CYS cc_start: 0.8245 (m) cc_final: 0.7672 (m) REVERT: R 288 ASN cc_start: 0.8109 (m-40) cc_final: 0.7184 (m110) outliers start: 25 outliers final: 11 residues processed: 122 average time/residue: 0.9666 time to fit residues: 125.9328 Evaluate side-chains 112 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 L residue 55 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN H 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086658 restraints weight = 12936.875| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.37 r_work: 0.3189 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7315 Z= 0.338 Angle : 0.723 9.962 9939 Z= 0.364 Chirality : 0.046 0.167 1135 Planarity : 0.004 0.054 1250 Dihedral : 5.383 49.629 1030 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.11 % Allowed : 21.89 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.28), residues: 904 helix: 0.09 (0.29), residues: 314 sheet: -0.91 (0.34), residues: 238 loop : -1.58 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 111 HIS 0.003 0.001 HIS H 214 PHE 0.011 0.001 PHE R 289 TYR 0.033 0.002 TYR R 69 ARG 0.006 0.001 ARG L 19 *********************** 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 113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7982 (t0) cc_final: 0.7219 (t0) REVERT: H 79 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8416 (mtpt) REVERT: H 92 GLU cc_start: 0.8885 (pm20) cc_final: 0.8549 (pm20) REVERT: H 119 GLN cc_start: 0.8965 (pt0) cc_final: 0.8707 (pp30) REVERT: H 185 GLN cc_start: 0.8729 (tt0) cc_final: 0.8476 (mt0) REVERT: H 209 ILE cc_start: 0.8745 (pt) cc_final: 0.8475 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8433 (mt-10) REVERT: K 31 ARG cc_start: 0.8495 (ptm160) cc_final: 0.7964 (ttp-170) REVERT: K 46 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7740 (mp0) REVERT: K 87 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7451 (mmtm) REVERT: K 101 ASP cc_start: 0.8731 (t0) cc_final: 0.8286 (t0) REVERT: L 107 GLU cc_start: 0.8454 (pt0) cc_final: 0.8004 (pt0) REVERT: R 34 MET cc_start: 0.4068 (ttt) cc_final: 0.3477 (ttt) REVERT: R 202 PHE cc_start: 0.8109 (t80) cc_final: 0.7503 (m-10) REVERT: R 1091 GLU cc_start: 0.8412 (mp0) cc_final: 0.7851 (mp0) REVERT: R 243 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.5996 (t80) REVERT: R 285 CYS cc_start: 0.8289 (m) cc_final: 0.7675 (m) outliers start: 24 outliers final: 16 residues processed: 106 average time/residue: 1.0073 time to fit residues: 114.0614 Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 12 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 115 THR 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 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 87 optimal weight: 0.0030 chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089977 restraints weight = 12915.915| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.40 r_work: 0.3245 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7315 Z= 0.191 Angle : 0.688 10.400 9939 Z= 0.345 Chirality : 0.044 0.160 1135 Planarity : 0.004 0.056 1250 Dihedral : 5.107 47.961 1030 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.46 % Allowed : 22.67 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 904 helix: 0.23 (0.29), residues: 314 sheet: -0.74 (0.34), residues: 231 loop : -1.43 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 111 HIS 0.002 0.001 HIS R 281 PHE 0.009 0.001 PHE L 141 TYR 0.012 0.001 TYR R 298 ARG 0.007 0.000 ARG L 19 *********************** 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 115 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8352 (tt0) cc_final: 0.8019 (pt0) REVERT: H 76 ASP cc_start: 0.7983 (t0) cc_final: 0.7247 (t0) REVERT: H 79 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8548 (mtpt) REVERT: H 92 GLU cc_start: 0.8871 (pm20) cc_final: 0.8552 (pm20) REVERT: H 119 GLN cc_start: 0.8927 (pt0) cc_final: 0.8720 (pp30) REVERT: H 185 GLN cc_start: 0.8730 (tt0) cc_final: 0.8453 (mt0) REVERT: H 209 ILE cc_start: 0.8784 (pt) cc_final: 0.8511 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8402 (mt-10) REVERT: K 31 ARG cc_start: 0.8501 (ptm160) cc_final: 0.8140 (ttm170) REVERT: K 46 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7768 (mp0) REVERT: K 87 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7360 (mmtm) REVERT: K 101 ASP cc_start: 0.8706 (t0) cc_final: 0.8030 (t0) REVERT: L 107 GLU cc_start: 0.8459 (pt0) cc_final: 0.8009 (pt0) REVERT: R 34 MET cc_start: 0.3967 (ttt) cc_final: 0.3315 (ttt) REVERT: R 146 GLU cc_start: 0.6983 (pp20) cc_final: 0.6716 (pp20) REVERT: R 198 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6151 (mt) REVERT: R 202 PHE cc_start: 0.8138 (t80) cc_final: 0.7519 (m-10) REVERT: R 1091 GLU cc_start: 0.8366 (mp0) cc_final: 0.7816 (mp0) REVERT: R 243 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.5752 (t80) REVERT: R 285 CYS cc_start: 0.8205 (m) cc_final: 0.7673 (m) REVERT: R 287 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7640 (tpt) REVERT: R 288 ASN cc_start: 0.8027 (m110) cc_final: 0.6865 (m110) outliers start: 19 outliers final: 11 residues processed: 108 average time/residue: 0.9896 time to fit residues: 114.1669 Evaluate side-chains 107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 243 PHE 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 24 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 23 optimal weight: 0.0060 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.136889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.091166 restraints weight = 13088.920| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.42 r_work: 0.3264 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7315 Z= 0.176 Angle : 0.694 10.505 9939 Z= 0.347 Chirality : 0.044 0.237 1135 Planarity : 0.004 0.057 1250 Dihedral : 4.915 41.224 1030 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.07 % Allowed : 23.83 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 904 helix: 0.41 (0.29), residues: 314 sheet: -0.57 (0.34), residues: 231 loop : -1.42 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 111 HIS 0.006 0.001 HIS R 147 PHE 0.009 0.001 PHE L 141 TYR 0.011 0.001 TYR R 298 ARG 0.007 0.000 ARG L 19 ********************** 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 118 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8342 (tt0) cc_final: 0.8024 (pt0) REVERT: H 76 ASP cc_start: 0.7984 (t0) cc_final: 0.7268 (t0) REVERT: H 79 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8673 (mtpm) REVERT: H 92 GLU cc_start: 0.8845 (pm20) cc_final: 0.8529 (pm20) REVERT: H 119 GLN cc_start: 0.8902 (pt0) cc_final: 0.8696 (pp30) REVERT: H 185 GLN cc_start: 0.8728 (tt0) cc_final: 0.8470 (mt0) REVERT: H 209 ILE cc_start: 0.8793 (pt) cc_final: 0.8506 (pp) REVERT: H 226 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8401 (mt-10) REVERT: K 31 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8196 (ttm170) REVERT: K 46 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7714 (mp0) REVERT: K 87 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7307 (mmtm) REVERT: K 101 ASP cc_start: 0.8695 (t0) cc_final: 0.8019 (t0) REVERT: K 104 TYR cc_start: 0.8899 (m-80) cc_final: 0.8699 (m-80) REVERT: L 107 GLU cc_start: 0.8464 (pt0) cc_final: 0.8031 (pt0) REVERT: L 149 GLN cc_start: 0.8603 (mt0) cc_final: 0.8351 (mt0) REVERT: R 34 MET cc_start: 0.3935 (ttt) cc_final: 0.3368 (ttt) REVERT: R 202 PHE cc_start: 0.8152 (t80) cc_final: 0.7522 (m-10) REVERT: R 1091 GLU cc_start: 0.8369 (mp0) cc_final: 0.7818 (mp0) REVERT: R 243 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.5855 (t80) REVERT: R 284 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7280 (p) REVERT: R 285 CYS cc_start: 0.8223 (m) cc_final: 0.7725 (m) REVERT: R 288 ASN cc_start: 0.7640 (m110) cc_final: 0.6488 (m110) outliers start: 16 outliers final: 9 residues processed: 112 average time/residue: 1.0493 time to fit residues: 125.1799 Evaluate side-chains 108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 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 240 ILE Chi-restraints excluded: chain R residue 243 PHE 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 70 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN R 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.136081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090222 restraints weight = 12859.216| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.39 r_work: 0.3246 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7315 Z= 0.212 Angle : 0.708 10.632 9939 Z= 0.354 Chirality : 0.045 0.252 1135 Planarity : 0.004 0.056 1250 Dihedral : 4.973 39.690 1030 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.59 % Allowed : 23.06 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.29), residues: 904 helix: 0.44 (0.30), residues: 314 sheet: -0.64 (0.34), residues: 235 loop : -1.32 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 111 HIS 0.002 0.001 HIS H 38 PHE 0.010 0.001 PHE R 289 TYR 0.014 0.001 TYR L 142 ARG 0.006 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5784.75 seconds wall clock time: 100 minutes 43.92 seconds (6043.92 seconds total)