Starting phenix.real_space_refine on Sat Jun 7 06:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.map" model { file = "/net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wj5_32543/06_2025/7wj5_32543.cif" } resolution = 3.72 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= 1.033 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 65 5.16 5 C 5551 2.51 5 N 1476 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.39, per 1000 atoms: 0.62 Number of scatterers: 8660 At special positions: 0 Unit cell: (106.112, 124.35, 117.718, 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 65 16.00 O 1568 8.00 N 1476 7.00 C 5551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 35.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.895A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.209A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.735A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.560A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.776A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.902A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.822A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 106 removed outlier: 4.283A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.055A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.658A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'R' and resid 251 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.891A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.569A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.291A 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: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.791A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.345A 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: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.270A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AB7, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.544A pdb=" N PHE S 7 " --> pdb=" O THR S 10 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 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: 2.82 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2743 1.34 - 1.46: 2191 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8846 Sorted by residual: bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.516 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.06e-01 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 7.01e-01 bond pdb=" CG1 ILE R 209 " pdb=" CD1 ILE R 209 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.79e-01 bond pdb=" C ILE A 264 " pdb=" N ILE A 265 " ideal model delta sigma weight residual 1.327 1.304 0.023 2.97e-02 1.13e+03 5.99e-01 ... (remaining 8841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11837 1.79 - 3.58: 133 3.58 - 5.37: 15 5.37 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 11994 Sorted by residual: angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 115.83 -6.02 2.21e+00 2.05e-01 7.42e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" C ARG R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.91e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4868 16.60 - 33.19: 297 33.19 - 49.79: 47 49.79 - 66.38: 7 66.38 - 82.98: 1 Dihedral angle restraints: 5220 sinusoidal: 1953 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N THR A 321 " pdb=" CA THR A 321 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 844 0.032 - 0.064: 374 0.064 - 0.096: 112 0.096 - 0.127: 46 0.127 - 0.159: 6 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1379 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 287 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO R 288 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 108 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 109 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 344 2.72 - 3.26: 8665 3.26 - 3.81: 14372 3.81 - 4.35: 17028 4.35 - 4.90: 30051 Nonbonded interactions: 70460 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.173 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" O SER R 244 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.206 3.040 nonbonded pdb=" O LYS A 349 " pdb=" ND2 ASN R 318 " model vdw 2.244 3.120 ... (remaining 70455 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 group one per residue 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: 1.240 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.004 0.035 8850 Z= 0.161 Angle : 0.547 8.958 12002 Z= 0.288 Chirality : 0.041 0.159 1382 Planarity : 0.003 0.031 1495 Dihedral : 10.788 82.979 3102 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 7.63 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.33 (0.30), residues: 283 loop : -0.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 107 PHE 0.012 0.001 PHE E 27 TYR 0.010 0.001 TYR R 211 ARG 0.002 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.11251 ( 426) hydrogen bonds : angle 5.58782 ( 1242) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.00454 ( 8) covalent geometry : bond 0.00365 ( 8846) covalent geometry : angle 0.54618 (11994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6043 (mmt) cc_final: 0.5559 (mpp) REVERT: B 57 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7614 (mtpt) REVERT: B 59 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: B 75 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 76 ASP cc_start: 0.8563 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 267 ASP cc_start: 0.7322 (m-30) cc_final: 0.6784 (m-30) REVERT: R 51 PHE cc_start: 0.7190 (m-10) cc_final: 0.6873 (m-10) REVERT: R 180 TYR cc_start: 0.7496 (m-10) cc_final: 0.7110 (m-10) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.2148 time to fit residues: 64.4627 Evaluate side-chains 189 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127563 restraints weight = 11214.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129871 restraints weight = 9255.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131050 restraints weight = 7316.977| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8850 Z= 0.141 Angle : 0.564 8.422 12002 Z= 0.294 Chirality : 0.042 0.153 1382 Planarity : 0.004 0.031 1495 Dihedral : 5.705 59.956 1238 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 10.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.04 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 350 sheet: 0.43 (0.30), residues: 280 loop : -0.21 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE A 250 TYR 0.015 0.001 TYR A 320 ARG 0.003 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 426) hydrogen bonds : angle 4.66227 ( 1242) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.92262 ( 8) covalent geometry : bond 0.00317 ( 8846) covalent geometry : angle 0.56368 (11994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.6011 (mmt) cc_final: 0.5806 (tpp) REVERT: B 57 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7629 (mtpt) REVERT: B 59 TYR cc_start: 0.8354 (m-80) cc_final: 0.8111 (m-80) REVERT: B 234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: R 51 PHE cc_start: 0.7097 (m-10) cc_final: 0.6841 (m-10) REVERT: R 180 TYR cc_start: 0.7315 (m-10) cc_final: 0.6950 (m-10) REVERT: R 251 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5436 (mp0) outliers start: 28 outliers final: 18 residues processed: 202 average time/residue: 0.2102 time to fit residues: 58.0110 Evaluate side-chains 185 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 overall best weight: 0.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN E 167 GLN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131035 restraints weight = 11366.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132693 restraints weight = 9170.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133521 restraints weight = 7596.044| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8850 Z= 0.100 Angle : 0.514 7.473 12002 Z= 0.272 Chirality : 0.041 0.147 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.855 58.511 1231 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.59 % Allowed : 11.22 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 355 sheet: 0.63 (0.30), residues: 258 loop : -0.30 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE A 189 TYR 0.013 0.001 TYR E 178 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 426) hydrogen bonds : angle 4.38972 ( 1242) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.64656 ( 8) covalent geometry : bond 0.00210 ( 8846) covalent geometry : angle 0.51394 (11994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7807 (tt0) cc_final: 0.7233 (tt0) REVERT: A 208 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.6356 (mmp80) REVERT: B 57 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7623 (mtpt) REVERT: B 76 ASP cc_start: 0.8382 (p0) cc_final: 0.8075 (p0) REVERT: B 234 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 267 ASP cc_start: 0.7211 (m-30) cc_final: 0.6637 (m-30) REVERT: R 51 PHE cc_start: 0.7093 (m-10) cc_final: 0.6838 (m-10) REVERT: R 116 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7204 (mtp85) REVERT: R 270 LEU cc_start: 0.8606 (tp) cc_final: 0.8295 (tp) outliers start: 33 outliers final: 20 residues processed: 202 average time/residue: 0.2101 time to fit residues: 57.4967 Evaluate side-chains 194 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129043 restraints weight = 11357.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130751 restraints weight = 9244.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131604 restraints weight = 7230.976| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8850 Z= 0.135 Angle : 0.546 8.026 12002 Z= 0.285 Chirality : 0.041 0.148 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.828 59.607 1227 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 3.92 % Allowed : 13.40 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 342 sheet: 0.40 (0.30), residues: 266 loop : -0.22 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE E 27 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 426) hydrogen bonds : angle 4.43205 ( 1242) SS BOND : bond 0.00399 ( 4) SS BOND : angle 2.20687 ( 8) covalent geometry : bond 0.00308 ( 8846) covalent geometry : angle 0.54370 (11994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 1.066 Fit side-chains REVERT: A 208 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.6329 (mmp80) REVERT: B 57 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7647 (mtpt) REVERT: B 76 ASP cc_start: 0.8327 (p0) cc_final: 0.8079 (p0) REVERT: B 234 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: B 267 ASP cc_start: 0.7215 (m-30) cc_final: 0.6661 (m-30) REVERT: C 40 TYR cc_start: 0.8195 (t80) cc_final: 0.7957 (t80) REVERT: E 206 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7254 (ptp90) REVERT: R 51 PHE cc_start: 0.7102 (m-10) cc_final: 0.6813 (m-10) REVERT: R 153 TRP cc_start: 0.5936 (OUTLIER) cc_final: 0.5461 (m-10) REVERT: R 248 LYS cc_start: 0.6967 (mtmm) cc_final: 0.6746 (mptt) outliers start: 36 outliers final: 27 residues processed: 199 average time/residue: 0.2267 time to fit residues: 60.6697 Evaluate side-chains 192 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 84 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124915 restraints weight = 11334.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126590 restraints weight = 9226.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127519 restraints weight = 7255.821| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8850 Z= 0.206 Angle : 0.608 9.360 12002 Z= 0.318 Chirality : 0.043 0.167 1382 Planarity : 0.004 0.032 1495 Dihedral : 5.140 59.526 1227 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 4.47 % Allowed : 14.27 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 342 sheet: 0.13 (0.30), residues: 277 loop : -0.21 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 197 HIS 0.003 0.001 HIS R 107 PHE 0.014 0.002 PHE E 27 TYR 0.012 0.002 TYR B 59 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 426) hydrogen bonds : angle 4.63591 ( 1242) SS BOND : bond 0.00358 ( 4) SS BOND : angle 1.86522 ( 8) covalent geometry : bond 0.00479 ( 8846) covalent geometry : angle 0.60582 (11994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6232 (mmp80) REVERT: B 57 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7724 (mtpt) REVERT: B 59 TYR cc_start: 0.8448 (m-80) cc_final: 0.8173 (m-80) REVERT: B 76 ASP cc_start: 0.8286 (p0) cc_final: 0.8026 (p0) REVERT: B 234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: B 267 ASP cc_start: 0.7186 (m-30) cc_final: 0.6663 (m-30) REVERT: B 290 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: E 206 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7247 (ptp90) REVERT: R 51 PHE cc_start: 0.7132 (m-10) cc_final: 0.6858 (m-10) REVERT: R 74 MET cc_start: 0.4908 (mmp) cc_final: 0.4143 (ppp) REVERT: R 153 TRP cc_start: 0.5888 (OUTLIER) cc_final: 0.5324 (m-10) REVERT: R 194 THR cc_start: 0.7862 (t) cc_final: 0.7657 (t) REVERT: R 248 LYS cc_start: 0.7031 (mtmm) cc_final: 0.6814 (mptt) outliers start: 41 outliers final: 28 residues processed: 200 average time/residue: 0.2199 time to fit residues: 60.0682 Evaluate side-chains 199 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127598 restraints weight = 11296.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129169 restraints weight = 9099.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130477 restraints weight = 7584.236| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8850 Z= 0.146 Angle : 0.556 8.250 12002 Z= 0.293 Chirality : 0.042 0.151 1382 Planarity : 0.003 0.032 1495 Dihedral : 4.992 59.223 1227 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 4.03 % Allowed : 15.47 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 343 sheet: 0.08 (0.30), residues: 279 loop : -0.19 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 197 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE E 27 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 426) hydrogen bonds : angle 4.51792 ( 1242) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.50165 ( 8) covalent geometry : bond 0.00334 ( 8846) covalent geometry : angle 0.55530 (11994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6235 (mmp80) REVERT: B 57 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7673 (mtpt) REVERT: B 75 GLN cc_start: 0.8129 (mt0) cc_final: 0.7413 (mt0) REVERT: B 76 ASP cc_start: 0.8311 (p0) cc_final: 0.8095 (p0) REVERT: B 234 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: E 206 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7309 (ptp90) REVERT: R 51 PHE cc_start: 0.7147 (m-10) cc_final: 0.6862 (m-10) REVERT: R 68 ILE cc_start: 0.8214 (mt) cc_final: 0.7511 (mt) REVERT: R 153 TRP cc_start: 0.5921 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: R 194 THR cc_start: 0.7777 (t) cc_final: 0.7477 (t) REVERT: R 248 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6787 (mptt) outliers start: 37 outliers final: 28 residues processed: 199 average time/residue: 0.2159 time to fit residues: 58.7803 Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131059 restraints weight = 11386.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132518 restraints weight = 9119.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133722 restraints weight = 7607.938| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8850 Z= 0.104 Angle : 0.523 8.090 12002 Z= 0.277 Chirality : 0.041 0.185 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.701 58.349 1227 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 3.49 % Allowed : 17.21 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.86 (0.26), residues: 1111 helix: 2.04 (0.28), residues: 349 sheet: 0.34 (0.31), residues: 253 loop : -0.29 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 197 HIS 0.002 0.000 HIS R 107 PHE 0.011 0.001 PHE A 334 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 426) hydrogen bonds : angle 4.39050 ( 1242) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.07965 ( 8) covalent geometry : bond 0.00224 ( 8846) covalent geometry : angle 0.52252 (11994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6177 (mmp80) REVERT: A 223 PHE cc_start: 0.7881 (t80) cc_final: 0.7658 (t80) REVERT: B 57 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7555 (mtpt) REVERT: B 59 TYR cc_start: 0.8392 (m-80) cc_final: 0.8120 (m-80) REVERT: B 165 THR cc_start: 0.7929 (p) cc_final: 0.7580 (t) REVERT: B 234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 267 ASP cc_start: 0.7261 (m-30) cc_final: 0.6674 (m-30) REVERT: E 206 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7320 (ptp90) REVERT: R 51 PHE cc_start: 0.7124 (m-10) cc_final: 0.6783 (m-10) REVERT: R 131 PHE cc_start: 0.6572 (m-80) cc_final: 0.6351 (m-80) REVERT: R 153 TRP cc_start: 0.5957 (OUTLIER) cc_final: 0.5481 (m-10) REVERT: R 174 ILE cc_start: 0.8146 (pt) cc_final: 0.7921 (pt) REVERT: R 305 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7742 (t) outliers start: 32 outliers final: 25 residues processed: 204 average time/residue: 0.2118 time to fit residues: 58.9400 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131368 restraints weight = 11568.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133540 restraints weight = 8886.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134681 restraints weight = 7399.040| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8850 Z= 0.113 Angle : 0.553 11.700 12002 Z= 0.291 Chirality : 0.041 0.176 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.663 57.575 1227 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.59 % Allowed : 18.74 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.83 (0.26), residues: 1111 helix: 1.89 (0.28), residues: 350 sheet: 0.36 (0.31), residues: 253 loop : -0.24 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 197 HIS 0.002 0.001 HIS B 225 PHE 0.010 0.001 PHE A 334 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 426) hydrogen bonds : angle 4.38825 ( 1242) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.17273 ( 8) covalent geometry : bond 0.00253 ( 8846) covalent geometry : angle 0.55256 (11994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.112 Fit side-chains REVERT: A 208 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6517 (ptp90) REVERT: A 223 PHE cc_start: 0.7846 (t80) cc_final: 0.7635 (t80) REVERT: B 57 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7429 (mtpt) REVERT: B 59 TYR cc_start: 0.8311 (m-80) cc_final: 0.7967 (m-80) REVERT: B 101 MET cc_start: 0.8566 (mmt) cc_final: 0.8221 (mmt) REVERT: B 234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: B 273 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8322 (mm) REVERT: R 153 TRP cc_start: 0.5935 (OUTLIER) cc_final: 0.5462 (m-10) REVERT: R 305 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7672 (t) outliers start: 33 outliers final: 26 residues processed: 198 average time/residue: 0.2537 time to fit residues: 69.0369 Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126064 restraints weight = 11611.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127457 restraints weight = 9637.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128492 restraints weight = 8541.998| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8850 Z= 0.220 Angle : 0.646 11.257 12002 Z= 0.337 Chirality : 0.044 0.180 1382 Planarity : 0.004 0.033 1495 Dihedral : 5.144 58.243 1227 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.81 % Allowed : 18.85 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.62 (0.25), residues: 1111 helix: 1.78 (0.28), residues: 343 sheet: -0.04 (0.30), residues: 278 loop : -0.21 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 197 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.002 PHE E 27 TYR 0.012 0.002 TYR R 180 ARG 0.011 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 426) hydrogen bonds : angle 4.69538 ( 1242) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.46348 ( 8) covalent geometry : bond 0.00517 ( 8846) covalent geometry : angle 0.64503 (11994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.084 Fit side-chains REVERT: A 208 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6490 (ptp90) REVERT: B 57 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7731 (mtpt) REVERT: B 234 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: R 153 TRP cc_start: 0.5834 (OUTLIER) cc_final: 0.5291 (m-10) REVERT: R 305 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7767 (t) outliers start: 35 outliers final: 26 residues processed: 196 average time/residue: 0.2343 time to fit residues: 64.3828 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.0170 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN R 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128458 restraints weight = 11425.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130018 restraints weight = 9492.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130924 restraints weight = 7393.404| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8850 Z= 0.129 Angle : 0.575 11.791 12002 Z= 0.301 Chirality : 0.042 0.185 1382 Planarity : 0.004 0.035 1495 Dihedral : 4.904 57.545 1227 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 3.27 % Allowed : 19.39 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.26), residues: 1111 helix: 1.82 (0.28), residues: 350 sheet: 0.06 (0.30), residues: 267 loop : -0.25 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE R 127 TYR 0.010 0.001 TYR E 178 ARG 0.008 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 426) hydrogen bonds : angle 4.51181 ( 1242) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.18022 ( 8) covalent geometry : bond 0.00294 ( 8846) covalent geometry : angle 0.57396 (11994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.931 Fit side-chains REVERT: A 208 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6357 (ptp90) REVERT: A 223 PHE cc_start: 0.7900 (t80) cc_final: 0.7669 (t80) REVERT: B 57 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7580 (mtpt) REVERT: B 59 TYR cc_start: 0.8372 (m-80) cc_final: 0.7827 (m-80) REVERT: B 101 MET cc_start: 0.8630 (mmt) cc_final: 0.7859 (mmt) REVERT: B 234 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: E 206 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7115 (ptp90) REVERT: R 153 TRP cc_start: 0.5899 (OUTLIER) cc_final: 0.5437 (m-10) REVERT: R 305 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7694 (t) outliers start: 30 outliers final: 26 residues processed: 195 average time/residue: 0.2150 time to fit residues: 57.5770 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129592 restraints weight = 11476.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131341 restraints weight = 9599.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132261 restraints weight = 7423.766| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8850 Z= 0.127 Angle : 0.578 11.879 12002 Z= 0.302 Chirality : 0.043 0.296 1382 Planarity : 0.004 0.039 1495 Dihedral : 4.873 57.058 1227 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.16 % Allowed : 20.04 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.68 (0.26), residues: 1111 helix: 1.78 (0.28), residues: 350 sheet: 0.15 (0.31), residues: 256 loop : -0.26 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 211 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE R 127 TYR 0.012 0.001 TYR R 273 ARG 0.008 0.000 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 426) hydrogen bonds : angle 4.45898 ( 1242) SS BOND : bond 0.00279 ( 4) SS BOND : angle 1.15506 ( 8) covalent geometry : bond 0.00288 ( 8846) covalent geometry : angle 0.57700 (11994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.90 seconds wall clock time: 57 minutes 30.48 seconds (3450.48 seconds total)