Starting phenix.real_space_refine on Thu Mar 13 15:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3s_41010/03_2025/8t3s_41010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3s_41010/03_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_41010/03_2025/8t3s_41010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3s_41010/03_2025/8t3s_41010.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3s_41010/03_2025/8t3s_41010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3s_41010/03_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-5624/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: 8.07, per 1000 atoms: 0.92 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: 2.89 Conformation dependent library (CDL) restraints added in 1.1 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: 1.10 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: 3.89 Time building geometry restraints manager: 3.44 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 27.680 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- 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 8956 Z= 0.322 Angle : 0.748 8.283 12148 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 *********************** 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 : 0.909 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.2405 time to fit residues: 45.2541 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 : 0.904 ------------------------------------------------------------------------------- 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: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115313 restraints weight = 9696.037| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.24 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.193 Angle : 0.523 8.000 12148 Z= 0.280 Chirality : 0.042 0.141 1378 Planarity : 0.004 0.067 1536 Dihedral : 4.733 57.644 1314 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.13 % Allowed : 20.38 % Favored : 77.48 % 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: 1.14 (0.26), residues: 1099 helix: 1.90 (0.26), residues: 376 sheet: 0.20 (0.31), residues: 272 loop : 0.26 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.024 0.001 PHE R 18 TYR 0.020 0.002 TYR R 14 ARG 0.003 0.000 ARG A 132 *********************** 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 159 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.873 Fit side-chains REVERT: A 83 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8585 (ttp) REVERT: B 59 TYR cc_start: 0.8268 (m-80) cc_final: 0.7437 (m-80) REVERT: N 87 ARG cc_start: 0.6825 (ptp-170) cc_final: 0.6476 (ptp-170) REVERT: R 243 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8387 (mp) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 0.2281 time to fit residues: 45.2118 Evaluate side-chains 138 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET 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 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 243 LEU 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: 0.8980 chunk 89 optimal weight: 0.0050 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.164884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120780 restraints weight = 9834.306| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.17 r_work: 0.3157 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8956 Z= 0.166 Angle : 0.488 9.110 12148 Z= 0.255 Chirality : 0.041 0.149 1378 Planarity : 0.004 0.058 1536 Dihedral : 4.393 57.246 1312 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.63 % Allowed : 20.17 % Favored : 76.20 % 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: 2.17 (0.26), residues: 379 sheet: 0.16 (0.31), residues: 273 loop : 0.32 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS A 209 PHE 0.028 0.001 PHE N 68 TYR 0.017 0.001 TYR R 165 ARG 0.004 0.000 ARG B 219 *********************** 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 178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.892 Fit side-chains REVERT: B 59 TYR cc_start: 0.8444 (m-80) cc_final: 0.7535 (m-80) REVERT: B 338 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8455 (mm) REVERT: G 62 ARG cc_start: 0.5957 (ptp90) cc_final: 0.5723 (ptp90) REVERT: R 106 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7291 (tm-30) outliers start: 34 outliers final: 18 residues processed: 165 average time/residue: 0.2261 time to fit residues: 51.4229 Evaluate side-chains 152 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE 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 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: 0.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.163508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119015 restraints weight = 9744.346| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.16 r_work: 0.3129 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.180 Angle : 0.489 8.262 12148 Z= 0.254 Chirality : 0.041 0.165 1378 Planarity : 0.003 0.053 1536 Dihedral : 4.285 52.322 1312 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.09 % Allowed : 21.02 % Favored : 75.88 % 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: 1.37 (0.25), residues: 1099 helix: 2.35 (0.26), residues: 374 sheet: 0.12 (0.31), residues: 273 loop : 0.30 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 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 *********************** 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 167 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.912 Fit side-chains REVERT: A 122 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 59 TYR cc_start: 0.8468 (m-80) cc_final: 0.7603 (m-80) REVERT: B 338 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8467 (mm) REVERT: N 161 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7011 (mtp85) REVERT: R 106 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7295 (tm-30) outliers start: 29 outliers final: 22 residues processed: 153 average time/residue: 0.2569 time to fit residues: 54.2846 Evaluate side-chains 158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 127 SER 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 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 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 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: 8.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 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 = 0.3794 r_free = 0.3794 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113578 restraints weight = 9731.991| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.20 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8956 Z= 0.260 Angle : 0.523 8.328 12148 Z= 0.271 Chirality : 0.042 0.174 1378 Planarity : 0.004 0.051 1536 Dihedral : 4.582 50.309 1312 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.59 % Allowed : 19.85 % Favored : 75.56 % 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 (0.26), residues: 1099 helix: 2.28 (0.26), residues: 381 sheet: 0.07 (0.30), residues: 282 loop : 0.27 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.025 0.002 PHE N 68 TYR 0.015 0.002 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** 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 177 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.970 Fit side-chains REVERT: A 122 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 161 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8816 (t) REVERT: B 338 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8573 (mm) REVERT: N 161 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7133 (mtp85) REVERT: N 192 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7096 (mtt90) REVERT: N 231 MET cc_start: 0.9341 (ttt) cc_final: 0.9109 (ttp) REVERT: R 106 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7449 (tm-30) outliers start: 43 outliers final: 28 residues processed: 163 average time/residue: 0.2531 time to fit residues: 56.6453 Evaluate side-chains 160 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 127 SER 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 100 VAL 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 275 SER Chi-restraints excluded: chain B residue 315 VAL 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 63 THR 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: 0.9980 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 31 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.162747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116420 restraints weight = 9665.705| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.22 r_work: 0.3120 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8956 Z= 0.162 Angle : 0.486 9.220 12148 Z= 0.250 Chirality : 0.040 0.182 1378 Planarity : 0.003 0.050 1536 Dihedral : 4.293 42.159 1312 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.95 % Allowed : 21.24 % 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: 1.44 (0.26), residues: 1099 helix: 2.51 (0.26), residues: 374 sheet: 0.09 (0.30), residues: 283 loop : 0.31 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.020 0.001 PHE R 18 TYR 0.015 0.001 TYR R 165 ARG 0.002 0.000 ARG B 219 *********************** 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 169 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.943 Fit side-chains REVERT: A 122 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 132 ARG cc_start: 0.8471 (mtm180) cc_final: 0.7985 (ptt180) REVERT: B 59 TYR cc_start: 0.8582 (m-80) cc_final: 0.7830 (m-80) REVERT: N 161 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7100 (mtp85) REVERT: N 192 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6984 (mtt180) REVERT: N 231 MET cc_start: 0.9278 (ttt) cc_final: 0.9055 (ttp) REVERT: R 45 HIS cc_start: 0.7393 (m90) cc_final: 0.6788 (m90) REVERT: R 106 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7439 (tm-30) outliers start: 37 outliers final: 24 residues processed: 155 average time/residue: 0.2236 time to fit residues: 47.1034 Evaluate side-chains 152 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 33 ILE Chi-restraints excluded: chain B residue 135 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 322 ASP Chi-restraints excluded: chain B residue 331 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 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: 7.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.161777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115659 restraints weight = 9735.030| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.20 r_work: 0.3104 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.193 Angle : 0.496 9.507 12148 Z= 0.256 Chirality : 0.041 0.159 1378 Planarity : 0.003 0.048 1536 Dihedral : 4.278 37.056 1312 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.59 % Allowed : 20.70 % 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: 1.44 (0.26), residues: 1099 helix: 2.45 (0.26), residues: 381 sheet: 0.07 (0.30), residues: 282 loop : 0.33 (0.31), residues: 436 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 0.023 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.002 0.000 ARG B 197 *********************** 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 171 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 132 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7989 (ptt180) REVERT: B 338 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8520 (mm) REVERT: N 161 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7110 (mtp85) REVERT: N 192 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7002 (mtt180) REVERT: R 12 MET cc_start: 0.7490 (ptm) cc_final: 0.7253 (ptm) REVERT: R 45 HIS cc_start: 0.7409 (m90) cc_final: 0.6778 (m90) REVERT: R 106 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7440 (tm-30) outliers start: 43 outliers final: 32 residues processed: 156 average time/residue: 0.2282 time to fit residues: 48.2941 Evaluate side-chains 161 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 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 88 ASN Chi-restraints excluded: chain B residue 100 VAL 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112817 restraints weight = 9924.092| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.22 r_work: 0.3060 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8956 Z= 0.250 Angle : 0.522 10.021 12148 Z= 0.270 Chirality : 0.042 0.150 1378 Planarity : 0.003 0.048 1536 Dihedral : 4.547 32.643 1312 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.70 % Allowed : 20.06 % Favored : 75.24 % 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: 2.43 (0.26), residues: 381 sheet: -0.02 (0.31), residues: 269 loop : 0.26 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.024 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.002 0.000 ARG B 197 *********************** 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 174 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 132 ARG cc_start: 0.8439 (mtm180) cc_final: 0.7986 (ptt180) REVERT: B 101 MET cc_start: 0.9139 (mtp) cc_final: 0.8933 (mtp) REVERT: B 172 GLU cc_start: 0.8493 (tp30) cc_final: 0.8204 (tp30) REVERT: B 338 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8624 (mm) REVERT: N 161 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7127 (mtp85) REVERT: N 192 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7054 (mtt90) REVERT: R 12 MET cc_start: 0.7492 (ptm) cc_final: 0.7254 (ptm) REVERT: R 187 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7755 (mp) outliers start: 44 outliers final: 34 residues processed: 158 average time/residue: 0.2156 time to fit residues: 46.7255 Evaluate side-chains 165 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 88 ASN Chi-restraints excluded: chain B residue 100 VAL 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 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113097 restraints weight = 9866.155| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.19 r_work: 0.3036 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8956 Z= 0.307 Angle : 0.543 10.142 12148 Z= 0.281 Chirality : 0.043 0.184 1378 Planarity : 0.004 0.047 1536 Dihedral : 4.781 40.303 1312 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.27 % Allowed : 21.02 % 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: 1.28 (0.26), residues: 1099 helix: 2.35 (0.26), residues: 381 sheet: -0.05 (0.32), residues: 251 loop : 0.20 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.002 PHE R 18 TYR 0.014 0.002 TYR R 165 ARG 0.003 0.000 ARG B 197 *********************** 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 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 132 ARG cc_start: 0.8427 (mtm180) cc_final: 0.7953 (ptt180) REVERT: B 101 MET cc_start: 0.9124 (mtp) cc_final: 0.8911 (mtp) REVERT: B 172 GLU cc_start: 0.8537 (tp30) cc_final: 0.8236 (tp30) REVERT: B 338 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8608 (mm) REVERT: N 161 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7040 (mtp85) REVERT: N 192 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7093 (mtt90) REVERT: R 12 MET cc_start: 0.7497 (ptm) cc_final: 0.7255 (ptm) REVERT: R 106 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: R 187 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7774 (mp) outliers start: 40 outliers final: 34 residues processed: 154 average time/residue: 0.2261 time to fit residues: 47.3314 Evaluate side-chains 162 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 88 ASN Chi-restraints excluded: chain B residue 100 VAL 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 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL 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 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 135 VAL 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: 0.9980 chunk 90 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 99 optimal weight: 0.0770 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 259 GLN N 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117524 restraints weight = 9707.502| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.25 r_work: 0.3098 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8956 Z= 0.147 Angle : 0.489 8.782 12148 Z= 0.253 Chirality : 0.040 0.195 1378 Planarity : 0.003 0.047 1536 Dihedral : 4.272 30.920 1312 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.84 % Allowed : 21.66 % Favored : 74.49 % 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: 1.50 (0.26), residues: 1099 helix: 2.60 (0.26), residues: 374 sheet: 0.17 (0.31), residues: 276 loop : 0.26 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 82 PHE 0.022 0.001 PHE R 18 TYR 0.013 0.001 TYR N 191 ARG 0.002 0.000 ARG B 197 ********************** 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 163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.906 Fit side-chains REVERT: A 122 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 132 ARG cc_start: 0.8410 (mtm180) cc_final: 0.8004 (ptt180) REVERT: B 172 GLU cc_start: 0.8452 (tp30) cc_final: 0.8126 (tp30) REVERT: B 246 ASP cc_start: 0.8551 (m-30) cc_final: 0.8301 (m-30) REVERT: B 331 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8885 (t) REVERT: B 338 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8535 (mm) REVERT: N 161 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.6896 (mtp85) REVERT: N 192 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6879 (mtt180) REVERT: R 12 MET cc_start: 0.7500 (ptm) cc_final: 0.7237 (ptm) REVERT: R 45 HIS cc_start: 0.7294 (m90) cc_final: 0.6644 (m90) REVERT: R 106 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7387 (tm-30) outliers start: 36 outliers final: 27 residues processed: 152 average time/residue: 0.2313 time to fit residues: 48.0889 Evaluate side-chains 158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 88 ASN Chi-restraints excluded: chain B residue 161 SER 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 315 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.160225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116571 restraints weight = 9798.065| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.23 r_work: 0.3084 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8956 Z= 0.226 Angle : 0.515 9.991 12148 Z= 0.266 Chirality : 0.042 0.184 1378 Planarity : 0.003 0.047 1536 Dihedral : 4.383 31.750 1312 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.84 % Allowed : 21.77 % Favored : 74.39 % 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: 1.40 (0.26), residues: 1099 helix: 2.47 (0.26), residues: 381 sheet: 0.13 (0.31), residues: 272 loop : 0.19 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 82 PHE 0.026 0.001 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5987.01 seconds wall clock time: 105 minutes 19.73 seconds (6319.73 seconds total)