Starting phenix.real_space_refine on Wed Feb 12 05:40:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tuy_26135/02_2025/7tuy_26135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tuy_26135/02_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_26135/02_2025/7tuy_26135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tuy_26135/02_2025/7tuy_26135.map" model { file = "/net/cci-nas-00/data/ceres_data/7tuy_26135/02_2025/7tuy_26135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tuy_26135/02_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-5592/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: 5.85, per 1000 atoms: 0.82 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: 1.87 Conformation dependent library (CDL) restraints added in 1.6 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: 0.92 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: 2.33 Time building geometry restraints manager: 2.07 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: 2.590 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- 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 : 0.783 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: 1.2037 time to fit residues: 187.5034 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 : 0.865 ------------------------------------------------------------------------------- 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 = 0.136848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091557 restraints weight = 12803.759| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.33 r_work: 0.3268 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8047 (t0) cc_final: 0.7472 (OUTLIER) REVERT: H 79 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8552 (mtpt) REVERT: H 92 GLU cc_start: 0.8841 (pm20) cc_final: 0.8527 (pm20) REVERT: H 119 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: H 185 GLN cc_start: 0.8863 (tt0) cc_final: 0.8564 (mt0) REVERT: H 209 ILE cc_start: 0.8747 (pt) cc_final: 0.8484 (pp) REVERT: H 226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8533 (mt-10) REVERT: K 31 ARG cc_start: 0.8310 (ptm160) cc_final: 0.7925 (ttp-170) REVERT: K 34 MET cc_start: 0.8223 (mmt) cc_final: 0.7971 (mmt) REVERT: K 46 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7776 (mp0) REVERT: K 74 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: K 98 ILE cc_start: 0.8625 (tp) cc_final: 0.8322 (tp) REVERT: K 101 ASP cc_start: 0.8753 (t0) cc_final: 0.8230 (t0) REVERT: L 107 GLU cc_start: 0.8421 (pt0) cc_final: 0.7884 (pt0) REVERT: L 124 ASP cc_start: 0.9073 (p0) cc_final: 0.8851 (OUTLIER) REVERT: L 128 LYS cc_start: 0.9228 (mptt) cc_final: 0.8950 (mmtm) REVERT: L 192 LYS cc_start: 0.8669 (pttp) cc_final: 0.8277 (mmtt) REVERT: L 213 ARG cc_start: 0.7106 (tpt90) cc_final: 0.6837 (tpt90) REVERT: R 34 MET cc_start: 0.3447 (ttt) cc_final: 0.3204 (ttt) REVERT: R 198 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6088 (mt) REVERT: R 202 PHE cc_start: 0.7983 (t80) cc_final: 0.7350 (m-10) REVERT: R 1091 GLU cc_start: 0.8259 (mp0) cc_final: 0.7813 (mp0) REVERT: R 288 ASN cc_start: 0.8100 (m110) cc_final: 0.7232 (m110) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 1.2059 time to fit residues: 160.6052 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 : 0.830 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4038 r_free = 0.4038 target = 0.136544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090608 restraints weight = 13017.274| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.38 r_work: 0.3254 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7315 Z= 0.193 Angle : 0.653 9.260 9939 Z= 0.330 Chirality : 0.044 0.163 1135 Planarity : 0.004 0.047 1250 Dihedral : 5.430 53.844 1030 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.11 % Allowed : 15.28 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.03 (0.27), residues: 904 helix: -0.21 (0.28), residues: 313 sheet: -1.53 (0.32), residues: 238 loop : -2.14 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 111 HIS 0.003 0.001 HIS R 281 PHE 0.007 0.001 PHE L 141 TYR 0.017 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 130 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7988 (t0) cc_final: 0.7332 (t0) REVERT: H 79 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8500 (mtpt) REVERT: H 92 GLU cc_start: 0.8843 (pm20) cc_final: 0.8501 (pm20) REVERT: H 119 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8673 (pt0) REVERT: H 185 GLN cc_start: 0.8840 (tt0) cc_final: 0.8536 (mt0) REVERT: H 209 ILE cc_start: 0.8779 (pt) cc_final: 0.8516 (pp) REVERT: H 226 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8515 (mt-10) REVERT: K 31 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8037 (ttm170) REVERT: K 34 MET cc_start: 0.8104 (mmt) cc_final: 0.7877 (mmt) REVERT: K 46 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7752 (mp0) REVERT: K 98 ILE cc_start: 0.8701 (tp) cc_final: 0.8278 (tp) REVERT: K 101 ASP cc_start: 0.8754 (t0) cc_final: 0.8134 (t0) REVERT: L 107 GLU cc_start: 0.8456 (pt0) cc_final: 0.7972 (pt0) REVERT: L 124 ASP cc_start: 0.9089 (p0) cc_final: 0.8799 (m-30) REVERT: L 128 LYS cc_start: 0.9238 (mptt) cc_final: 0.9007 (mmtm) REVERT: L 192 LYS cc_start: 0.8421 (pttp) cc_final: 0.8147 (mmtt) REVERT: R 34 MET cc_start: 0.3776 (ttt) cc_final: 0.3142 (ttt) REVERT: R 156 TRP cc_start: 0.8169 (t-100) cc_final: 0.7914 (m100) REVERT: R 198 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6161 (mt) REVERT: R 202 PHE cc_start: 0.8020 (t80) cc_final: 0.7415 (m-10) REVERT: R 1091 GLU cc_start: 0.8327 (mp0) cc_final: 0.7847 (mp0) REVERT: R 287 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7715 (ttm) REVERT: R 288 ASN cc_start: 0.8119 (m-40) cc_final: 0.7496 (m110) REVERT: R 294 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6937 (t70) outliers start: 24 outliers final: 7 residues processed: 120 average time/residue: 1.0682 time to fit residues: 136.2104 Evaluate side-chains 110 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 HIS R 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.133180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088894 restraints weight = 12584.005| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.21 r_work: 0.3219 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7315 Z= 0.266 Angle : 0.675 8.588 9939 Z= 0.343 Chirality : 0.044 0.171 1135 Planarity : 0.004 0.050 1250 Dihedral : 5.362 50.024 1030 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.85 % Allowed : 17.36 % Favored : 79.79 % 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: -1.77 (0.28), residues: 904 helix: -0.06 (0.29), residues: 314 sheet: -1.40 (0.31), residues: 256 loop : -1.92 (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 0.008 0.001 PHE L 63 TYR 0.018 0.001 TYR R 69 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 121 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8042 (t0) cc_final: 0.7391 (t0) REVERT: H 79 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8532 (mtpt) REVERT: H 92 GLU cc_start: 0.8900 (pm20) cc_final: 0.8547 (pm20) REVERT: H 119 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: H 185 GLN cc_start: 0.8816 (tt0) cc_final: 0.8565 (mt0) REVERT: H 209 ILE cc_start: 0.8828 (pt) cc_final: 0.8561 (pp) REVERT: H 226 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8499 (mt-10) REVERT: K 31 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8045 (ttm170) REVERT: K 46 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7823 (mp0) REVERT: K 101 ASP cc_start: 0.8737 (t0) cc_final: 0.8324 (t0) REVERT: L 107 GLU cc_start: 0.8462 (pt0) cc_final: 0.7916 (pt0) REVERT: L 192 LYS cc_start: 0.8343 (pttp) cc_final: 0.8078 (mmtt) REVERT: R 34 MET cc_start: 0.3895 (ttt) cc_final: 0.3551 (ttt) REVERT: R 156 TRP cc_start: 0.8210 (t-100) cc_final: 0.7949 (m100) REVERT: R 198 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6180 (mt) REVERT: R 202 PHE cc_start: 0.8078 (t80) cc_final: 0.7510 (m-10) REVERT: R 1091 GLU cc_start: 0.8362 (mp0) cc_final: 0.7905 (mp0) REVERT: R 285 CYS cc_start: 0.8313 (m) cc_final: 0.7682 (m) REVERT: R 288 ASN cc_start: 0.8204 (m-40) cc_final: 0.7294 (m110) outliers start: 22 outliers final: 10 residues processed: 115 average time/residue: 1.0929 time to fit residues: 133.6556 Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 7 SER 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 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 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: 8.9990 chunk 34 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.136789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090722 restraints weight = 12818.138| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.37 r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2563 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= 0.171 Angle : 0.654 10.142 9939 Z= 0.325 Chirality : 0.043 0.184 1135 Planarity : 0.004 0.055 1250 Dihedral : 5.023 42.944 1030 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.11 % Allowed : 18.13 % Favored : 78.76 % 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: -1.48 (0.28), residues: 904 helix: 0.12 (0.29), residues: 315 sheet: -1.12 (0.33), residues: 231 loop : -1.79 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 111 HIS 0.002 0.001 HIS R 281 PHE 0.007 0.001 PHE L 141 TYR 0.013 0.001 TYR R 69 ARG 0.006 0.000 ARG L 213 *********************** 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 125 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8279 (tt0) cc_final: 0.8004 (tt0) REVERT: H 76 ASP cc_start: 0.7985 (t0) cc_final: 0.7284 (t0) REVERT: H 79 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8545 (mtpt) REVERT: H 92 GLU cc_start: 0.8843 (pm20) cc_final: 0.8500 (pm20) REVERT: H 185 GLN cc_start: 0.8782 (tt0) cc_final: 0.8515 (mt0) REVERT: H 209 ILE cc_start: 0.8811 (pt) cc_final: 0.8544 (pp) REVERT: H 226 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8483 (mt-10) REVERT: K 31 ARG cc_start: 0.8371 (ptm160) cc_final: 0.8042 (ttm170) REVERT: K 34 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8035 (mmp) REVERT: K 46 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7751 (mp0) REVERT: K 87 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7719 (mtmm) REVERT: K 101 ASP cc_start: 0.8708 (t0) cc_final: 0.8084 (t0) REVERT: L 107 GLU cc_start: 0.8478 (pt0) cc_final: 0.8043 (pt0) REVERT: L 192 LYS cc_start: 0.8332 (pttp) cc_final: 0.8014 (mmtt) REVERT: R 34 MET cc_start: 0.3823 (ttt) cc_final: 0.3206 (ttt) REVERT: R 156 TRP cc_start: 0.8121 (t-100) cc_final: 0.7839 (m100) REVERT: R 198 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6104 (mt) REVERT: R 202 PHE cc_start: 0.8077 (t80) cc_final: 0.7513 (m-10) REVERT: R 1091 GLU cc_start: 0.8347 (mp0) cc_final: 0.7859 (mp0) REVERT: R 243 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: R 285 CYS cc_start: 0.8288 (m) cc_final: 0.7714 (m) REVERT: R 288 ASN cc_start: 0.8214 (m-40) cc_final: 0.7431 (m110) outliers start: 24 outliers final: 7 residues processed: 120 average time/residue: 1.0109 time to fit residues: 129.4419 Evaluate side-chains 102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 34 MET 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 243 PHE 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 74 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.137858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092076 restraints weight = 12802.363| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.37 r_work: 0.3285 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7315 Z= 0.163 Angle : 0.649 9.632 9939 Z= 0.323 Chirality : 0.042 0.166 1135 Planarity : 0.004 0.055 1250 Dihedral : 4.712 32.897 1030 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.24 % Allowed : 19.04 % Favored : 77.72 % 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: 0.37 (0.30), residues: 314 sheet: -0.98 (0.32), residues: 241 loop : -1.64 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 111 HIS 0.003 0.000 HIS H 214 PHE 0.009 0.001 PHE R 289 TYR 0.017 0.001 TYR R 69 ARG 0.005 0.000 ARG L 213 *********************** 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 129 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7987 (t0) cc_final: 0.7297 (t0) REVERT: H 79 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8582 (mtpt) REVERT: H 92 GLU cc_start: 0.8821 (pm20) cc_final: 0.8494 (pm20) REVERT: H 185 GLN cc_start: 0.8750 (tt0) cc_final: 0.8505 (mt0) REVERT: H 209 ILE cc_start: 0.8843 (pt) cc_final: 0.8573 (pp) REVERT: H 226 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8488 (mt-10) REVERT: K 31 ARG cc_start: 0.8526 (ptm160) cc_final: 0.8216 (ttm170) REVERT: K 46 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7706 (mp0) REVERT: K 101 ASP cc_start: 0.8704 (t0) cc_final: 0.8133 (t0) REVERT: K 104 TYR cc_start: 0.8925 (m-80) cc_final: 0.8713 (m-80) REVERT: L 107 GLU cc_start: 0.8446 (pt0) cc_final: 0.8044 (pt0) REVERT: L 192 LYS cc_start: 0.8338 (pttp) cc_final: 0.7976 (mmtt) REVERT: R 34 MET cc_start: 0.3699 (ttt) cc_final: 0.3374 (ttt) REVERT: R 146 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6641 (pp20) REVERT: R 156 TRP cc_start: 0.8145 (t-100) cc_final: 0.7901 (m100) REVERT: R 198 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6150 (mt) REVERT: R 202 PHE cc_start: 0.8035 (t80) cc_final: 0.7487 (m-10) REVERT: R 1091 GLU cc_start: 0.8317 (mp0) cc_final: 0.7745 (mp0) REVERT: R 243 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: R 285 CYS cc_start: 0.8292 (m) cc_final: 0.7692 (m) REVERT: R 288 ASN cc_start: 0.8066 (m-40) cc_final: 0.7201 (m110) outliers start: 25 outliers final: 8 residues processed: 123 average time/residue: 1.0543 time to fit residues: 138.2668 Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 69 optimal weight: 0.0270 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.137457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091540 restraints weight = 12824.477| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.38 r_work: 0.3270 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7315 Z= 0.180 Angle : 0.661 10.363 9939 Z= 0.329 Chirality : 0.044 0.198 1135 Planarity : 0.004 0.056 1250 Dihedral : 4.691 29.786 1030 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.07 % Allowed : 20.98 % Favored : 76.94 % 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: -1.16 (0.29), residues: 904 helix: 0.35 (0.29), residues: 315 sheet: -0.95 (0.32), residues: 242 loop : -1.56 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 111 HIS 0.002 0.000 HIS R 281 PHE 0.007 0.001 PHE L 141 TYR 0.033 0.001 TYR R 69 ARG 0.007 0.000 ARG L 19 *********************** 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 113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7985 (t0) cc_final: 0.7250 (t0) REVERT: H 79 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8555 (mtpt) REVERT: H 92 GLU cc_start: 0.8819 (pm20) cc_final: 0.8486 (pm20) REVERT: H 185 GLN cc_start: 0.8745 (tt0) cc_final: 0.8462 (mt0) REVERT: H 209 ILE cc_start: 0.8871 (pt) cc_final: 0.8602 (pp) REVERT: H 226 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8486 (mt-10) REVERT: K 31 ARG cc_start: 0.8516 (ptm160) cc_final: 0.8199 (ttm170) REVERT: K 46 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7709 (mp0) REVERT: K 87 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7508 (mtmm) REVERT: K 101 ASP cc_start: 0.8694 (t0) cc_final: 0.8121 (t0) REVERT: L 80 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8472 (mm110) REVERT: L 149 GLN cc_start: 0.8585 (mt0) cc_final: 0.8343 (mt0) REVERT: L 192 LYS cc_start: 0.8305 (pttp) cc_final: 0.7907 (mmtt) REVERT: L 213 ARG cc_start: 0.7399 (tpt90) cc_final: 0.7191 (tpt90) REVERT: R 34 MET cc_start: 0.3704 (ttt) cc_final: 0.3187 (ttt) REVERT: R 198 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6191 (mt) REVERT: R 202 PHE cc_start: 0.8020 (t80) cc_final: 0.7461 (m-10) REVERT: R 1091 GLU cc_start: 0.8346 (mp0) cc_final: 0.7769 (mp0) REVERT: R 243 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6980 (OUTLIER) REVERT: R 284 VAL cc_start: 0.7660 (t) cc_final: 0.7370 (p) REVERT: R 285 CYS cc_start: 0.8333 (m) cc_final: 0.7768 (m) REVERT: R 288 ASN cc_start: 0.8150 (m-40) cc_final: 0.7287 (m110) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.1147 time to fit residues: 129.0916 Evaluate side-chains 105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR 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 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 243 PHE 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 88 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.135344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088929 restraints weight = 12935.554| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.40 r_work: 0.3229 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7315 Z= 0.252 Angle : 0.694 10.988 9939 Z= 0.347 Chirality : 0.044 0.173 1135 Planarity : 0.004 0.055 1250 Dihedral : 4.871 33.559 1030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.33 % Allowed : 21.11 % Favored : 76.55 % 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: -1.17 (0.29), residues: 904 helix: 0.36 (0.30), residues: 310 sheet: -0.99 (0.32), residues: 248 loop : -1.53 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 281 PHE 0.010 0.001 PHE R 289 TYR 0.016 0.001 TYR L 142 ARG 0.006 0.000 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 108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8528 (tt0) cc_final: 0.8221 (pt0) REVERT: H 76 ASP cc_start: 0.7993 (t0) cc_final: 0.7252 (t0) REVERT: H 79 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: H 92 GLU cc_start: 0.8848 (pm20) cc_final: 0.8500 (pm20) REVERT: H 185 GLN cc_start: 0.8749 (tt0) cc_final: 0.8490 (mt0) REVERT: H 209 ILE cc_start: 0.8861 (pt) cc_final: 0.8588 (pp) REVERT: H 226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8457 (mt-10) REVERT: K 31 ARG cc_start: 0.8541 (ptm160) cc_final: 0.8282 (ttm170) REVERT: K 46 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7761 (mp0) REVERT: K 87 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7508 (mtmm) REVERT: K 101 ASP cc_start: 0.8703 (t0) cc_final: 0.8026 (t0) REVERT: L 107 GLU cc_start: 0.8291 (pt0) cc_final: 0.7940 (pt0) REVERT: L 192 LYS cc_start: 0.8252 (pttp) cc_final: 0.7800 (mmtt) REVERT: R 34 MET cc_start: 0.3785 (ttt) cc_final: 0.3221 (ttt) REVERT: R 146 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6805 (pp20) REVERT: R 198 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6208 (mt) REVERT: R 202 PHE cc_start: 0.8057 (t80) cc_final: 0.7493 (m-10) REVERT: R 1091 GLU cc_start: 0.8378 (mp0) cc_final: 0.7824 (mp0) REVERT: R 243 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: R 288 ASN cc_start: 0.8200 (m-40) cc_final: 0.7311 (m110) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 1.1962 time to fit residues: 129.4114 Evaluate side-chains 100 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.133720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086990 restraints weight = 12955.596| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.39 r_work: 0.3195 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7315 Z= 0.317 Angle : 0.724 11.295 9939 Z= 0.362 Chirality : 0.045 0.188 1135 Planarity : 0.004 0.054 1250 Dihedral : 5.152 41.497 1030 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.59 % Allowed : 21.24 % 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 (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: -1.19 (0.28), residues: 904 helix: 0.27 (0.29), residues: 310 sheet: -0.95 (0.33), residues: 238 loop : -1.52 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 281 PHE 0.009 0.001 PHE L 100 TYR 0.016 0.001 TYR L 142 ARG 0.006 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 107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.8011 (t0) cc_final: 0.7253 (t0) REVERT: H 79 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8442 (mtpt) REVERT: H 92 GLU cc_start: 0.8900 (pm20) cc_final: 0.8587 (pm20) REVERT: H 185 GLN cc_start: 0.8739 (tt0) cc_final: 0.8452 (mt0) REVERT: H 209 ILE cc_start: 0.8765 (pt) cc_final: 0.8485 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8455 (mt-10) REVERT: K 31 ARG cc_start: 0.8563 (ptm160) cc_final: 0.8322 (ttm170) REVERT: K 46 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7764 (mp0) REVERT: K 87 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7522 (mtmm) REVERT: K 101 ASP cc_start: 0.8691 (t0) cc_final: 0.8022 (t0) REVERT: L 107 GLU cc_start: 0.8313 (pt0) cc_final: 0.7972 (pt0) REVERT: R 34 MET cc_start: 0.3897 (ttt) cc_final: 0.3322 (ttt) REVERT: R 202 PHE cc_start: 0.8167 (t80) cc_final: 0.7536 (m-10) REVERT: R 1091 GLU cc_start: 0.8428 (mp0) cc_final: 0.7908 (mp0) REVERT: R 243 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: R 285 CYS cc_start: 0.8319 (m) cc_final: 0.7684 (m) REVERT: R 288 ASN cc_start: 0.8374 (m-40) cc_final: 0.7481 (m110) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 1.1537 time to fit residues: 125.1048 Evaluate side-chains 101 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 165 THR 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 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 1005 LEU 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: 4.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090154 restraints weight = 13062.424| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.42 r_work: 0.3249 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7315 Z= 0.188 Angle : 0.690 11.770 9939 Z= 0.342 Chirality : 0.044 0.173 1135 Planarity : 0.004 0.056 1250 Dihedral : 4.905 37.926 1030 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.46 % Allowed : 21.11 % Favored : 76.42 % 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: -1.02 (0.29), residues: 904 helix: 0.38 (0.29), residues: 314 sheet: -0.79 (0.33), residues: 237 loop : -1.45 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS L 191 PHE 0.008 0.001 PHE R 289 TYR 0.014 0.001 TYR R 184 ARG 0.006 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 112 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8345 (tt0) cc_final: 0.8012 (pt0) REVERT: H 76 ASP cc_start: 0.7980 (t0) cc_final: 0.7249 (t0) REVERT: H 79 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8556 (mtpt) REVERT: H 92 GLU cc_start: 0.8876 (pm20) cc_final: 0.8554 (pm20) REVERT: H 185 GLN cc_start: 0.8737 (tt0) cc_final: 0.8466 (mt0) REVERT: H 209 ILE cc_start: 0.8840 (pt) cc_final: 0.8573 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8440 (mt-10) REVERT: K 31 ARG cc_start: 0.8520 (ptm160) cc_final: 0.8277 (ttm170) REVERT: K 46 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7759 (mp0) REVERT: K 87 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7290 (mtmm) REVERT: K 89 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: K 101 ASP cc_start: 0.8620 (t0) cc_final: 0.7954 (t0) REVERT: K 104 TYR cc_start: 0.8872 (m-80) cc_final: 0.8668 (m-80) REVERT: L 107 GLU cc_start: 0.8306 (pt0) cc_final: 0.7935 (pt0) REVERT: R 34 MET cc_start: 0.3762 (ttt) cc_final: 0.3437 (ttt) REVERT: R 198 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6185 (mm) REVERT: R 202 PHE cc_start: 0.8186 (t80) cc_final: 0.7574 (m-10) REVERT: R 1091 GLU cc_start: 0.8384 (mp0) cc_final: 0.7833 (mp0) REVERT: R 284 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7338 (p) REVERT: R 285 CYS cc_start: 0.8255 (m) cc_final: 0.7593 (m) REVERT: R 288 ASN cc_start: 0.8228 (m-40) cc_final: 0.7242 (m110) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 1.1498 time to fit residues: 129.5329 Evaluate side-chains 107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 165 THR 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 89 GLU 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 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 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: 7.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.136360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090109 restraints weight = 12837.781| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.38 r_work: 0.3246 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3202 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= 0.204 Angle : 0.695 11.902 9939 Z= 0.346 Chirality : 0.044 0.169 1135 Planarity : 0.004 0.056 1250 Dihedral : 4.885 34.880 1030 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.33 % Allowed : 21.63 % Favored : 76.04 % 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: -0.97 (0.29), residues: 904 helix: 0.43 (0.30), residues: 308 sheet: -0.74 (0.34), residues: 238 loop : -1.43 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.000 HIS R 281 PHE 0.007 0.001 PHE L 141 TYR 0.014 0.001 TYR R 184 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: 5171.37 seconds wall clock time: 92 minutes 40.64 seconds (5560.64 seconds total)