Starting phenix.real_space_refine on Mon May 12 12:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3s_41010/05_2025/8t3s_41010.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5600 2.51 5 N 1496 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1797 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2063 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 3 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'BUA': 1, 'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.45, per 1000 atoms: 0.62 Number of scatterers: 8769 At special positions: 0 Unit cell: (84.252, 123.9, 119.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1620 8.00 N 1496 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.527A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.895A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.522A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.026A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.512A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.613A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.757A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.037A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 38 Proline residue: R 23 - end of helix removed outlier: 3.607A pdb=" N GLN R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.526A pdb=" N LEU R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 72 removed outlier: 3.523A pdb=" N LYS R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 113 removed outlier: 3.718A pdb=" N TYR R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 121 Processing helix chain 'R' and resid 122 through 149 removed outlier: 3.908A pdb=" N GLY R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 187 removed outlier: 3.692A pdb=" N VAL R 176 " --> pdb=" O GLN R 172 " (cutoff:3.500A) Proline residue: R 178 - end of helix removed outlier: 3.533A pdb=" N CYS R 184 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 209 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.596A pdb=" N VAL R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Proline residue: R 237 - end of helix removed outlier: 3.524A pdb=" N SER R 241 " --> pdb=" O PRO R 237 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS R 242 " --> pdb=" O TYR R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 274 removed outlier: 3.869A pdb=" N VAL R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE R 261 " --> pdb=" O ILE R 257 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.386A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.256A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.713A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.814A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.665A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.932A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.465A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.410A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.741A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.378A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 147 through 149 removed outlier: 3.567A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1218 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: 2.58 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1425 1.32 - 1.44: 2464 1.44 - 1.57: 4991 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8956 Sorted by residual: bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.535 1.456 0.079 1.71e-02 3.42e+03 2.15e+01 bond pdb=" N GLN R 40 " pdb=" CA GLN R 40 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.534 1.445 0.090 2.47e-02 1.64e+03 1.32e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" CA SER R 92 " pdb=" CB SER R 92 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.10e+01 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11586 1.66 - 3.31: 447 3.31 - 4.97: 93 4.97 - 6.63: 17 6.63 - 8.28: 5 Bond angle restraints: 12148 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.89 104.61 8.28 1.24e+00 6.50e-01 4.46e+01 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " ideal model delta sigma weight residual 114.17 107.50 6.67 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N GLN B 75 " pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 113.21 106.62 6.59 1.15e+00 7.56e-01 3.28e+01 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 115.72 108.97 6.75 1.51e+00 4.39e-01 2.00e+01 angle pdb=" N ALA R 13 " pdb=" CA ALA R 13 " pdb=" C ALA R 13 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 1.99e+01 ... (remaining 12143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4701 17.98 - 35.95: 528 35.95 - 53.93: 117 53.93 - 71.90: 13 71.90 - 89.88: 3 Dihedral angle restraints: 5362 sinusoidal: 2120 harmonic: 3242 Sorted by residual: dihedral pdb=" C PRO R 252 " pdb=" N PRO R 252 " pdb=" CA PRO R 252 " pdb=" CB PRO R 252 " ideal model delta harmonic sigma weight residual -120.70 -110.61 -10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CA HIS B 311 " pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1183 0.067 - 0.135: 168 0.135 - 0.202: 22 0.202 - 0.270: 4 0.270 - 0.337: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU R 9 " pdb=" N LEU R 9 " pdb=" C LEU R 9 " pdb=" CB LEU R 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1375 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 86 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER R 86 " 0.059 2.00e-02 2.50e+03 pdb=" O SER R 86 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE R 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 62 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO R 63 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 63 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 63 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 13 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ALA R 13 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA R 13 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 14 " -0.015 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 516 2.73 - 3.27: 8733 3.27 - 3.81: 14843 3.81 - 4.36: 17894 4.36 - 4.90: 31450 Nonbonded interactions: 73436 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.185 3.040 nonbonded pdb=" O ALA R 133 " pdb=" OG SER R 137 " model vdw 2.196 3.040 nonbonded pdb=" O TYR R 238 " pdb=" OG SER R 241 " model vdw 2.227 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.253 3.040 ... (remaining 73431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.560 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.090 8959 Z= 0.319 Angle : 0.748 8.283 12154 Z= 0.498 Chirality : 0.051 0.337 1378 Planarity : 0.005 0.065 1536 Dihedral : 15.215 89.881 3261 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.53 % Allowed : 21.66 % Favored : 77.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.26), residues: 1099 helix: 1.51 (0.26), residues: 381 sheet: 0.16 (0.32), residues: 272 loop : 0.01 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 254 HIS 0.004 0.001 HIS A 214 PHE 0.028 0.002 PHE N 240 TYR 0.043 0.002 TYR R 14 ARG 0.016 0.001 ARG R 217 Details of bonding type rmsd hydrogen bonds : bond 0.20469 ( 429) hydrogen bonds : angle 7.38399 ( 1218) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.34839 ( 6) covalent geometry : bond 0.00502 ( 8956) covalent geometry : angle 0.74846 (12148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.966 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.2255 time to fit residues: 42.1212 Evaluate side-chains 131 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114565 restraints weight = 9703.312| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.22 r_work: 0.3148 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8959 Z= 0.142 Angle : 0.524 8.198 12154 Z= 0.280 Chirality : 0.042 0.144 1378 Planarity : 0.004 0.065 1536 Dihedral : 4.755 58.461 1314 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.77 % Allowed : 20.17 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.18 (0.26), residues: 1099 helix: 1.97 (0.26), residues: 373 sheet: 0.21 (0.31), residues: 272 loop : 0.28 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.023 0.002 PHE R 18 TYR 0.018 0.002 TYR R 14 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 429) hydrogen bonds : angle 4.95098 ( 1218) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.60392 ( 6) covalent geometry : bond 0.00316 ( 8956) covalent geometry : angle 0.52414 (12148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.878 Fit side-chains REVERT: B 59 TYR cc_start: 0.8334 (m-80) cc_final: 0.7417 (m-80) REVERT: N 87 ARG cc_start: 0.6802 (ptp-170) cc_final: 0.6554 (ptp-170) outliers start: 26 outliers final: 18 residues processed: 156 average time/residue: 0.2237 time to fit residues: 47.1985 Evaluate side-chains 145 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119384 restraints weight = 9832.917| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.17 r_work: 0.3136 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8959 Z= 0.121 Angle : 0.498 9.304 12154 Z= 0.260 Chirality : 0.041 0.163 1378 Planarity : 0.004 0.058 1536 Dihedral : 4.449 58.275 1312 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.31 % Allowed : 19.74 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.29 (0.25), residues: 1099 helix: 2.21 (0.26), residues: 373 sheet: 0.12 (0.30), residues: 275 loop : 0.31 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.024 0.001 PHE N 68 TYR 0.017 0.001 TYR R 165 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 429) hydrogen bonds : angle 4.49257 ( 1218) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.27396 ( 6) covalent geometry : bond 0.00276 ( 8956) covalent geometry : angle 0.49846 (12148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.922 Fit side-chains REVERT: B 59 TYR cc_start: 0.8486 (m-80) cc_final: 0.7627 (m-80) REVERT: B 338 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8492 (mm) REVERT: R 106 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7335 (tm-30) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 0.2118 time to fit residues: 45.6277 Evaluate side-chains 153 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 32 GLN B 156 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114926 restraints weight = 9735.914| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.25 r_work: 0.3093 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8959 Z= 0.142 Angle : 0.507 8.111 12154 Z= 0.263 Chirality : 0.042 0.166 1378 Planarity : 0.004 0.053 1536 Dihedral : 4.459 52.868 1312 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.84 % Allowed : 20.38 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.31 (0.25), residues: 1099 helix: 2.29 (0.26), residues: 374 sheet: 0.08 (0.30), residues: 271 loop : 0.28 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.016 0.001 PHE R 18 TYR 0.016 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 429) hydrogen bonds : angle 4.43012 ( 1218) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.42452 ( 6) covalent geometry : bond 0.00332 ( 8956) covalent geometry : angle 0.50690 (12148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.899 Fit side-chains REVERT: A 122 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 199 ASP cc_start: 0.8058 (m-30) cc_final: 0.7635 (m-30) REVERT: B 59 TYR cc_start: 0.8568 (m-80) cc_final: 0.7818 (m-80) REVERT: B 101 MET cc_start: 0.9121 (mtp) cc_final: 0.8856 (mtp) REVERT: B 338 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8514 (mm) REVERT: N 161 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7125 (mtp85) REVERT: R 106 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7427 (tm-30) outliers start: 36 outliers final: 23 residues processed: 163 average time/residue: 0.2108 time to fit residues: 47.3616 Evaluate side-chains 158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115495 restraints weight = 9685.956| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.38 r_work: 0.3114 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8959 Z= 0.121 Angle : 0.494 9.443 12154 Z= 0.254 Chirality : 0.041 0.173 1378 Planarity : 0.003 0.050 1536 Dihedral : 4.362 47.705 1312 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.27 % Allowed : 20.60 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.26), residues: 1099 helix: 2.31 (0.26), residues: 381 sheet: 0.12 (0.30), residues: 281 loop : 0.29 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.028 0.001 PHE N 68 TYR 0.015 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 429) hydrogen bonds : angle 4.32855 ( 1218) SS BOND : bond 0.00162 ( 3) SS BOND : angle 0.32895 ( 6) covalent geometry : bond 0.00282 ( 8956) covalent geometry : angle 0.49371 (12148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.984 Fit side-chains REVERT: A 122 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 132 ARG cc_start: 0.8433 (mtm180) cc_final: 0.7892 (ptt180) REVERT: A 199 ASP cc_start: 0.7969 (m-30) cc_final: 0.7552 (m-30) REVERT: B 59 TYR cc_start: 0.8574 (m-80) cc_final: 0.7768 (m-80) REVERT: B 101 MET cc_start: 0.9136 (mtp) cc_final: 0.8846 (mtp) REVERT: B 338 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8487 (mm) REVERT: N 161 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.6992 (mtp85) REVERT: N 192 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6899 (mtt180) REVERT: R 45 HIS cc_start: 0.7373 (m90) cc_final: 0.6698 (m90) REVERT: R 106 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7418 (tm-30) outliers start: 40 outliers final: 29 residues processed: 162 average time/residue: 0.2482 time to fit residues: 54.5634 Evaluate side-chains 161 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.164243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118370 restraints weight = 9649.241| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.21 r_work: 0.3143 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8959 Z= 0.096 Angle : 0.476 8.542 12154 Z= 0.244 Chirality : 0.040 0.154 1378 Planarity : 0.003 0.049 1536 Dihedral : 4.104 38.610 1312 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.84 % Allowed : 20.70 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.46 (0.26), residues: 1099 helix: 2.45 (0.26), residues: 381 sheet: 0.08 (0.30), residues: 294 loop : 0.39 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 PHE 0.022 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 429) hydrogen bonds : angle 4.18420 ( 1218) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.28356 ( 6) covalent geometry : bond 0.00215 ( 8956) covalent geometry : angle 0.47602 (12148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 132 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8029 (ptt180) REVERT: B 59 TYR cc_start: 0.8529 (m-80) cc_final: 0.7767 (m-80) REVERT: B 101 MET cc_start: 0.9069 (mtp) cc_final: 0.8868 (mtp) REVERT: B 338 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8438 (mm) REVERT: N 161 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7104 (mtp85) REVERT: N 192 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7056 (mtt180) REVERT: N 231 MET cc_start: 0.9269 (ttt) cc_final: 0.9032 (ttp) REVERT: R 45 HIS cc_start: 0.7335 (m90) cc_final: 0.6649 (m90) REVERT: R 106 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7480 (tm-30) outliers start: 36 outliers final: 22 residues processed: 159 average time/residue: 0.2208 time to fit residues: 47.8716 Evaluate side-chains 153 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116573 restraints weight = 9704.884| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.21 r_work: 0.3117 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8959 Z= 0.119 Angle : 0.484 9.876 12154 Z= 0.249 Chirality : 0.041 0.135 1378 Planarity : 0.003 0.050 1536 Dihedral : 4.138 34.721 1312 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.74 % Allowed : 21.45 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.26), residues: 1099 helix: 2.51 (0.26), residues: 381 sheet: 0.08 (0.30), residues: 283 loop : 0.35 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.021 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 429) hydrogen bonds : angle 4.18366 ( 1218) SS BOND : bond 0.00168 ( 3) SS BOND : angle 0.33240 ( 6) covalent geometry : bond 0.00277 ( 8956) covalent geometry : angle 0.48378 (12148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.878 Fit side-chains REVERT: A 122 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 132 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8037 (ptt180) REVERT: B 59 TYR cc_start: 0.8575 (m-80) cc_final: 0.7803 (m-80) REVERT: B 101 MET cc_start: 0.9141 (mtp) cc_final: 0.8867 (mtp) REVERT: B 338 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8471 (mm) REVERT: N 161 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7063 (mtp85) REVERT: N 192 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6955 (mtt180) REVERT: R 12 MET cc_start: 0.7498 (ptm) cc_final: 0.7264 (ptm) REVERT: R 45 HIS cc_start: 0.7355 (m90) cc_final: 0.6673 (m90) REVERT: R 106 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7501 (tm-30) outliers start: 35 outliers final: 27 residues processed: 152 average time/residue: 0.2222 time to fit residues: 45.6483 Evaluate side-chains 157 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117775 restraints weight = 9819.401| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.22 r_work: 0.3133 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8959 Z= 0.104 Angle : 0.472 9.342 12154 Z= 0.243 Chirality : 0.040 0.132 1378 Planarity : 0.003 0.049 1536 Dihedral : 4.016 27.909 1312 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.06 % Allowed : 21.02 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.62 (0.26), residues: 1099 helix: 2.69 (0.26), residues: 375 sheet: 0.17 (0.30), residues: 287 loop : 0.37 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.022 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 429) hydrogen bonds : angle 4.11217 ( 1218) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.28134 ( 6) covalent geometry : bond 0.00236 ( 8956) covalent geometry : angle 0.47213 (12148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.833 Fit side-chains REVERT: A 122 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 132 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8062 (ptt180) REVERT: B 59 TYR cc_start: 0.8573 (m-80) cc_final: 0.7801 (m-80) REVERT: B 101 MET cc_start: 0.9101 (mtp) cc_final: 0.8865 (mtp) REVERT: B 338 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8483 (mm) REVERT: N 161 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7077 (mtp85) REVERT: N 192 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7067 (mtt180) REVERT: N 231 MET cc_start: 0.9285 (ttt) cc_final: 0.9055 (ttp) REVERT: R 12 MET cc_start: 0.7491 (ptm) cc_final: 0.7252 (ptm) REVERT: R 45 HIS cc_start: 0.7338 (m90) cc_final: 0.6621 (m90) REVERT: R 106 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7487 (tm-30) outliers start: 38 outliers final: 30 residues processed: 152 average time/residue: 0.2309 time to fit residues: 46.9135 Evaluate side-chains 159 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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 = 0.3812 r_free = 0.3812 target = 0.161680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115199 restraints weight = 9804.312| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.22 r_work: 0.3092 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8959 Z= 0.133 Angle : 0.495 9.695 12154 Z= 0.256 Chirality : 0.041 0.136 1378 Planarity : 0.003 0.049 1536 Dihedral : 4.163 27.384 1312 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.38 % Allowed : 20.92 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.54 (0.26), residues: 1099 helix: 2.58 (0.26), residues: 384 sheet: 0.21 (0.30), residues: 274 loop : 0.26 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.023 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 429) hydrogen bonds : angle 4.21407 ( 1218) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.42264 ( 6) covalent geometry : bond 0.00313 ( 8956) covalent geometry : angle 0.49471 (12148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 132 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8065 (ptt180) REVERT: B 59 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: B 338 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8491 (mm) REVERT: N 161 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7098 (mtp85) REVERT: N 192 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.6923 (mtt180) REVERT: R 12 MET cc_start: 0.7495 (ptm) cc_final: 0.7255 (ptm) REVERT: R 45 HIS cc_start: 0.7397 (m90) cc_final: 0.6739 (m90) REVERT: R 106 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: R 187 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7743 (mp) outliers start: 41 outliers final: 33 residues processed: 153 average time/residue: 0.2385 time to fit residues: 50.0596 Evaluate side-chains 164 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.163536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117568 restraints weight = 9737.173| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.18 r_work: 0.3128 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8959 Z= 0.106 Angle : 0.479 9.213 12154 Z= 0.248 Chirality : 0.040 0.128 1378 Planarity : 0.003 0.049 1536 Dihedral : 4.041 26.769 1312 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.06 % Allowed : 21.02 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.64 (0.26), residues: 1099 helix: 2.71 (0.26), residues: 378 sheet: 0.26 (0.30), residues: 278 loop : 0.30 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 PHE 0.023 0.001 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 429) hydrogen bonds : angle 4.13695 ( 1218) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.26713 ( 6) covalent geometry : bond 0.00243 ( 8956) covalent geometry : angle 0.47920 (12148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.900 Fit side-chains REVERT: A 122 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 132 ARG cc_start: 0.8426 (mtm180) cc_final: 0.8050 (ptt180) REVERT: B 59 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: B 101 MET cc_start: 0.9108 (mtp) cc_final: 0.8853 (mtp) REVERT: B 338 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8457 (mm) REVERT: N 161 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7068 (mtp85) REVERT: N 192 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6971 (mtt180) REVERT: R 12 MET cc_start: 0.7483 (ptm) cc_final: 0.7234 (ptm) REVERT: R 45 HIS cc_start: 0.7365 (m90) cc_final: 0.6684 (m90) REVERT: R 106 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: R 187 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7763 (mp) outliers start: 38 outliers final: 28 residues processed: 147 average time/residue: 0.2198 time to fit residues: 43.8011 Evaluate side-chains 156 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 192 ARG Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113186 restraints weight = 9829.717| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.20 r_work: 0.3037 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8959 Z= 0.211 Angle : 0.551 10.846 12154 Z= 0.286 Chirality : 0.043 0.148 1378 Planarity : 0.004 0.049 1536 Dihedral : 4.622 37.134 1312 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.06 % Allowed : 21.13 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.39 (0.26), residues: 1099 helix: 2.46 (0.26), residues: 384 sheet: 0.03 (0.32), residues: 249 loop : 0.21 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS B 311 PHE 0.029 0.002 PHE R 18 TYR 0.013 0.002 TYR R 165 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 429) hydrogen bonds : angle 4.45592 ( 1218) SS BOND : bond 0.00102 ( 3) SS BOND : angle 0.71700 ( 6) covalent geometry : bond 0.00503 ( 8956) covalent geometry : angle 0.55044 (12148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5410.71 seconds wall clock time: 94 minutes 15.36 seconds (5655.36 seconds total)