Starting phenix.real_space_refine on Wed Mar 4 02:06:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.map" model { file = "/net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dw9_30877/03_2026/7dw9_30877.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 67 5.16 5 C 6423 2.51 5 N 1757 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10105 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2177 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1971 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.04, per 1000 atoms: 0.20 Number of scatterers: 10105 At special positions: 0 Unit cell: (131.88, 89.04, 118.44, 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 67 16.00 O 1858 8.00 N 1757 7.00 C 6423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 6 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 328.4 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 16 sheets defined 35.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 33 through 67 removed outlier: 4.586A pdb=" N ALA R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 92 Processing helix chain 'R' and resid 92 through 102 removed outlier: 3.706A pdb=" N THR R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 143 removed outlier: 4.242A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 171 removed outlier: 3.591A pdb=" N SER R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 200 through 214 removed outlier: 3.948A pdb=" N TYR R 205 " --> pdb=" O GLY R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 235 Processing helix chain 'R' and resid 264 through 297 Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 304 through 311 Processing helix chain 'R' and resid 312 through 314 No H-bonds generated for 'chain 'R' and resid 312 through 314' Processing helix chain 'R' and resid 315 through 329 removed outlier: 3.721A pdb=" N CYS R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 329 through 338 removed outlier: 3.762A pdb=" N GLU R 335 " --> pdb=" O SER R 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 39 removed outlier: 4.068A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.598A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'Y' and resid 7 through 25 removed outlier: 3.786A pdb=" N GLN Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE Y 25 " --> pdb=" O MET Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.625A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing helix chain 'Y' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.072A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.632A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.854A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.569A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.707A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.882A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.181A 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: 3.555A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.856A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.720A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.766A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.607A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.609A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.059A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.059A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB7, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.705A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.705A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1365 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: 1.69 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3286 1.34 - 1.46: 2513 1.46 - 1.58: 4436 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 10331 Sorted by residual: bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N THR Y 6 " pdb=" CA THR Y 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N THR R 31 " pdb=" CA THR R 31 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N CYS C 1 " pdb=" CA CYS C 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 ... (remaining 10326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13823 2.42 - 4.83: 181 4.83 - 7.25: 11 7.25 - 9.66: 6 9.66 - 12.08: 3 Bond angle restraints: 14024 Sorted by residual: angle pdb=" C14 CLR R 601 " pdb=" C8 CLR R 601 " pdb=" C7 CLR R 601 " ideal model delta sigma weight residual 110.19 122.27 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C14 CLR R 602 " pdb=" C8 CLR R 602 " pdb=" C7 CLR R 602 " ideal model delta sigma weight residual 110.19 122.20 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C14 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C7 CLR R 603 " ideal model delta sigma weight residual 110.19 121.54 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C7 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C9 CLR R 603 " ideal model delta sigma weight residual 110.39 119.43 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" C MET S 192 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 ... (remaining 14019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5869 17.86 - 35.72: 340 35.72 - 53.58: 44 53.58 - 71.44: 14 71.44 - 89.30: 9 Dihedral angle restraints: 6276 sinusoidal: 2562 harmonic: 3714 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA CYS C 1 " pdb=" C CYS C 1 " pdb=" N TYR C 2 " pdb=" CA TYR C 2 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.389: 1571 0.389 - 0.778: 0 0.778 - 1.167: 0 1.167 - 1.556: 0 1.556 - 1.945: 3 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C8 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C7 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.69 0.75 1.95 2.00e-01 2.50e+01 9.46e+01 chirality pdb=" C8 CLR R 603 " pdb=" C14 CLR R 603 " pdb=" C7 CLR R 603 " pdb=" C9 CLR R 603 " both_signs ideal model delta sigma weight residual False 2.69 0.77 1.93 2.00e-01 2.50e+01 9.26e+01 chirality pdb=" C8 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C7 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.69 0.80 1.89 2.00e-01 2.50e+01 8.93e+01 ... (remaining 1571 not shown) Planarity restraints: 1771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " 0.268 9.50e-02 1.11e+02 1.21e-01 1.06e+01 pdb=" NE ARG B 137 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.47e+00 pdb=" NE ARG B 150 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 47 " -0.002 2.00e-02 2.50e+03 1.70e-02 7.25e+00 pdb=" CG TRP S 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP S 47 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP S 47 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP S 47 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP S 47 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP S 47 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 47 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP S 47 " 0.006 2.00e-02 2.50e+03 ... (remaining 1768 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2980 2.83 - 3.34: 9546 3.34 - 3.86: 16042 3.86 - 4.38: 19541 4.38 - 4.90: 33724 Nonbonded interactions: 81833 Sorted by model distance: nonbonded pdb=" O GLY S 9 " pdb=" NH1 ARG S 18 " model vdw 2.306 3.120 nonbonded pdb=" OE1 GLU R 40 " pdb=" NZ LYS R 100 " model vdw 2.322 3.120 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.354 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.356 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.362 3.040 ... (remaining 81828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:9.610 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.006 0.101 10337 Z= 0.283 Angle : 0.772 12.081 14034 Z= 0.429 Chirality : 0.097 1.945 1574 Planarity : 0.009 0.121 1771 Dihedral : 12.291 89.296 3865 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.09 % Allowed : 0.84 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.22), residues: 1259 helix: -0.18 (0.24), residues: 395 sheet: 0.67 (0.26), residues: 340 loop : -0.15 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG B 137 TYR 0.027 0.005 TYR A 253 PHE 0.018 0.002 PHE B 235 TRP 0.042 0.005 TRP S 47 HIS 0.013 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00618 (10331) covalent geometry : angle 0.77103 (14024) SS BOND : bond 0.00924 ( 5) SS BOND : angle 1.52575 ( 10) hydrogen bonds : bond 0.20350 ( 488) hydrogen bonds : angle 7.01243 ( 1365) Misc. bond : bond 0.10135 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7200 (mmmt) REVERT: R 136 ASP cc_start: 0.8439 (t0) cc_final: 0.8176 (t0) REVERT: R 200 TRP cc_start: 0.7592 (m-10) cc_final: 0.7381 (m-10) REVERT: R 297 ASP cc_start: 0.7950 (t0) cc_final: 0.6876 (t0) REVERT: R 316 LEU cc_start: 0.8894 (tp) cc_final: 0.8517 (pt) REVERT: Y 58 GLU cc_start: 0.8159 (pm20) cc_final: 0.7646 (pm20) REVERT: Y 63 GLU cc_start: 0.7154 (tt0) cc_final: 0.6581 (tp30) REVERT: N 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7942 (t0) REVERT: N 76 LYS cc_start: 0.9217 (ttmm) cc_final: 0.9004 (ttmm) REVERT: S 18 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8583 (tpt-90) REVERT: S 73 ASP cc_start: 0.7282 (t70) cc_final: 0.7052 (t70) REVERT: S 83 MET cc_start: 0.9188 (mtm) cc_final: 0.8979 (mtp) REVERT: S 223 ASP cc_start: 0.8189 (m-30) cc_final: 0.7828 (m-30) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.7981 time to fit residues: 152.5481 Evaluate side-chains 136 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 91 HIS B 293 ASN N 3 GLN S 77 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.065246 restraints weight = 19312.010| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.04 r_work: 0.2777 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10337 Z= 0.122 Angle : 0.599 7.740 14034 Z= 0.319 Chirality : 0.043 0.175 1574 Planarity : 0.004 0.034 1771 Dihedral : 5.522 50.831 1602 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.12 % Allowed : 7.63 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1259 helix: 2.15 (0.26), residues: 390 sheet: 1.00 (0.28), residues: 320 loop : 0.23 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.018 0.001 TYR S 190 PHE 0.018 0.001 PHE B 292 TRP 0.023 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00256 (10331) covalent geometry : angle 0.59809 (14024) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.04522 ( 10) hydrogen bonds : bond 0.04540 ( 488) hydrogen bonds : angle 4.54476 ( 1365) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.356 Fit side-chains REVERT: R 136 ASP cc_start: 0.8834 (t0) cc_final: 0.8523 (t0) REVERT: R 297 ASP cc_start: 0.7716 (t0) cc_final: 0.6989 (t0) REVERT: R 313 LEU cc_start: 0.8121 (tp) cc_final: 0.7738 (tm) REVERT: R 319 CYS cc_start: 0.8937 (t) cc_final: 0.8628 (m) REVERT: A 299 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8660 (mp0) REVERT: B 172 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7749 (pp20) REVERT: B 215 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8568 (mm-30) REVERT: Y 32 LYS cc_start: 0.8174 (mptm) cc_final: 0.7954 (mtpm) REVERT: Y 36 ASP cc_start: 0.8458 (m-30) cc_final: 0.8159 (m-30) REVERT: Y 58 GLU cc_start: 0.8338 (pm20) cc_final: 0.7932 (pm20) REVERT: Y 63 GLU cc_start: 0.7538 (tt0) cc_final: 0.5983 (tm-30) REVERT: N 73 ASP cc_start: 0.8165 (t0) cc_final: 0.7639 (t0) REVERT: N 76 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8946 (ttmm) REVERT: S 46 GLU cc_start: 0.8535 (tt0) cc_final: 0.8301 (tt0) REVERT: S 73 ASP cc_start: 0.7213 (t70) cc_final: 0.5871 (t70) REVERT: S 76 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8699 (mtmm) REVERT: S 223 ASP cc_start: 0.8529 (m-30) cc_final: 0.8129 (m-30) REVERT: S 234 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8200 (pt0) outliers start: 12 outliers final: 1 residues processed: 164 average time/residue: 0.7237 time to fit residues: 125.3895 Evaluate side-chains 133 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 50.0000 chunk 115 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 317 ASN A 294 GLN N 3 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061261 restraints weight = 19178.104| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.00 r_work: 0.2678 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10337 Z= 0.194 Angle : 0.621 7.557 14034 Z= 0.328 Chirality : 0.044 0.188 1574 Planarity : 0.005 0.041 1771 Dihedral : 5.379 55.731 1599 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.49 % Allowed : 9.58 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1259 helix: 2.47 (0.26), residues: 397 sheet: 0.88 (0.27), residues: 332 loop : -0.00 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 317 TYR 0.019 0.002 TYR B 105 PHE 0.032 0.002 PHE B 292 TRP 0.017 0.001 TRP A 234 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00461 (10331) covalent geometry : angle 0.62042 (14024) SS BOND : bond 0.00634 ( 5) SS BOND : angle 1.30371 ( 10) hydrogen bonds : bond 0.04995 ( 488) hydrogen bonds : angle 4.37545 ( 1365) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.393 Fit side-chains REVERT: R 136 ASP cc_start: 0.8867 (t0) cc_final: 0.8593 (t0) REVERT: R 212 MET cc_start: 0.8849 (mmp) cc_final: 0.8482 (mmp) REVERT: R 297 ASP cc_start: 0.7791 (t0) cc_final: 0.7207 (t0) REVERT: A 59 GLN cc_start: 0.8453 (pp30) cc_final: 0.8163 (pp30) REVERT: A 299 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8643 (mp0) REVERT: B 172 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7813 (pp20) REVERT: B 217 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (pmm) REVERT: Y 32 LYS cc_start: 0.8272 (mptm) cc_final: 0.8009 (mtpm) REVERT: Y 36 ASP cc_start: 0.8452 (m-30) cc_final: 0.8179 (m-30) REVERT: Y 58 GLU cc_start: 0.8389 (pm20) cc_final: 0.8083 (pm20) REVERT: Y 63 GLU cc_start: 0.7656 (tt0) cc_final: 0.6028 (tm-30) REVERT: N 43 LYS cc_start: 0.7265 (ptmm) cc_final: 0.6932 (pptt) REVERT: N 46 GLU cc_start: 0.8713 (pt0) cc_final: 0.8473 (pt0) REVERT: N 73 ASP cc_start: 0.8253 (t0) cc_final: 0.7638 (t0) REVERT: N 76 LYS cc_start: 0.9375 (ttmm) cc_final: 0.8985 (ttmm) REVERT: S 46 GLU cc_start: 0.8554 (tt0) cc_final: 0.8270 (tt0) REVERT: S 73 ASP cc_start: 0.7255 (t70) cc_final: 0.7017 (t70) REVERT: S 234 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8415 (pt0) outliers start: 16 outliers final: 5 residues processed: 145 average time/residue: 0.7654 time to fit residues: 117.2591 Evaluate side-chains 135 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain S residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.062292 restraints weight = 19486.765| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.04 r_work: 0.2702 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10337 Z= 0.143 Angle : 0.568 8.058 14034 Z= 0.299 Chirality : 0.042 0.168 1574 Planarity : 0.004 0.034 1771 Dihedral : 5.104 59.880 1599 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.95 % Allowed : 11.07 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1259 helix: 2.64 (0.26), residues: 397 sheet: 0.86 (0.27), residues: 334 loop : -0.00 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.016 0.001 TYR S 190 PHE 0.027 0.001 PHE B 292 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 (10331) covalent geometry : angle 0.56800 (14024) SS BOND : bond 0.00475 ( 5) SS BOND : angle 1.02868 ( 10) hydrogen bonds : bond 0.04252 ( 488) hydrogen bonds : angle 4.16440 ( 1365) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.266 Fit side-chains REVERT: R 136 ASP cc_start: 0.8858 (t0) cc_final: 0.8555 (t0) REVERT: R 297 ASP cc_start: 0.7791 (t0) cc_final: 0.7242 (t0) REVERT: A 63 TYR cc_start: 0.7242 (m-10) cc_final: 0.7013 (m-10) REVERT: A 299 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8605 (mp0) REVERT: B 172 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: Y 32 LYS cc_start: 0.8260 (mptm) cc_final: 0.7997 (mtpp) REVERT: Y 36 ASP cc_start: 0.8547 (m-30) cc_final: 0.8267 (m-30) REVERT: Y 58 GLU cc_start: 0.8382 (pm20) cc_final: 0.8066 (pm20) REVERT: Y 63 GLU cc_start: 0.7681 (tt0) cc_final: 0.6041 (tm-30) REVERT: N 43 LYS cc_start: 0.7141 (ptmm) cc_final: 0.6896 (pptt) REVERT: N 46 GLU cc_start: 0.8672 (pt0) cc_final: 0.8454 (pt0) REVERT: N 73 ASP cc_start: 0.8261 (t0) cc_final: 0.7649 (t0) REVERT: N 76 LYS cc_start: 0.9405 (ttmm) cc_final: 0.9025 (ttmm) REVERT: S 46 GLU cc_start: 0.8534 (tt0) cc_final: 0.8290 (tt0) REVERT: S 73 ASP cc_start: 0.7264 (t70) cc_final: 0.7036 (t70) REVERT: S 82 GLN cc_start: 0.8509 (tp40) cc_final: 0.8061 (tp40) outliers start: 21 outliers final: 10 residues processed: 144 average time/residue: 0.7581 time to fit residues: 115.3577 Evaluate side-chains 141 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 21 MET Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain C residue 1 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 50.0000 chunk 3 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.060439 restraints weight = 19402.499| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.02 r_work: 0.2652 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10337 Z= 0.212 Angle : 0.616 8.118 14034 Z= 0.324 Chirality : 0.044 0.183 1574 Planarity : 0.004 0.032 1771 Dihedral : 5.210 57.894 1599 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 12.09 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1259 helix: 2.59 (0.26), residues: 398 sheet: 0.78 (0.27), residues: 334 loop : -0.08 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 218 TYR 0.018 0.002 TYR B 105 PHE 0.029 0.002 PHE B 292 TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00506 (10331) covalent geometry : angle 0.61497 (14024) SS BOND : bond 0.00657 ( 5) SS BOND : angle 1.22116 ( 10) hydrogen bonds : bond 0.04864 ( 488) hydrogen bonds : angle 4.24721 ( 1365) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.427 Fit side-chains REVERT: R 136 ASP cc_start: 0.8854 (t0) cc_final: 0.8565 (t0) REVERT: R 297 ASP cc_start: 0.7814 (t0) cc_final: 0.7231 (t0) REVERT: A 299 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8627 (mp0) REVERT: B 172 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: B 215 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 262 MET cc_start: 0.8860 (ttm) cc_final: 0.8513 (ttm) REVERT: B 303 ASP cc_start: 0.8523 (m-30) cc_final: 0.8307 (m-30) REVERT: Y 36 ASP cc_start: 0.8476 (m-30) cc_final: 0.8205 (m-30) REVERT: Y 58 GLU cc_start: 0.8434 (pm20) cc_final: 0.8137 (pm20) REVERT: Y 63 GLU cc_start: 0.7794 (tt0) cc_final: 0.6186 (tm-30) REVERT: N 43 LYS cc_start: 0.7214 (ptmm) cc_final: 0.6926 (pptt) REVERT: N 46 GLU cc_start: 0.8682 (pt0) cc_final: 0.8448 (pt0) REVERT: N 73 ASP cc_start: 0.8277 (t0) cc_final: 0.7650 (t0) REVERT: N 76 LYS cc_start: 0.9421 (ttmm) cc_final: 0.9037 (ttmm) REVERT: S 46 GLU cc_start: 0.8574 (tt0) cc_final: 0.8362 (tt0) REVERT: S 73 ASP cc_start: 0.7301 (t70) cc_final: 0.7076 (t70) REVERT: S 82 GLN cc_start: 0.8459 (tp40) cc_final: 0.8062 (tp40) outliers start: 24 outliers final: 11 residues processed: 146 average time/residue: 0.7580 time to fit residues: 117.0048 Evaluate side-chains 139 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain C residue 1 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.059763 restraints weight = 19455.732| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.05 r_work: 0.2651 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10337 Z= 0.239 Angle : 0.637 8.230 14034 Z= 0.336 Chirality : 0.045 0.186 1574 Planarity : 0.004 0.035 1771 Dihedral : 5.262 52.693 1599 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.42 % Allowed : 13.30 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1259 helix: 2.52 (0.26), residues: 398 sheet: 0.70 (0.27), residues: 339 loop : -0.21 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 317 TYR 0.017 0.002 TYR B 105 PHE 0.029 0.002 PHE B 292 TRP 0.017 0.001 TRP A 234 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00571 (10331) covalent geometry : angle 0.63671 (14024) SS BOND : bond 0.00707 ( 5) SS BOND : angle 1.23898 ( 10) hydrogen bonds : bond 0.05039 ( 488) hydrogen bonds : angle 4.29239 ( 1365) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.387 Fit side-chains REVERT: R 136 ASP cc_start: 0.8842 (t0) cc_final: 0.8560 (t0) REVERT: R 297 ASP cc_start: 0.7880 (t0) cc_final: 0.7286 (t0) REVERT: A 299 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8576 (mp0) REVERT: B 172 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: B 303 ASP cc_start: 0.8557 (m-30) cc_final: 0.8350 (m-30) REVERT: Y 32 LYS cc_start: 0.8503 (mtpm) cc_final: 0.8286 (mtpp) REVERT: Y 36 ASP cc_start: 0.8469 (m-30) cc_final: 0.8201 (m-30) REVERT: Y 58 GLU cc_start: 0.8441 (pm20) cc_final: 0.8160 (pm20) REVERT: Y 63 GLU cc_start: 0.7813 (tt0) cc_final: 0.6207 (tm-30) REVERT: N 73 ASP cc_start: 0.8327 (t0) cc_final: 0.7684 (t0) REVERT: N 76 LYS cc_start: 0.9431 (ttmm) cc_final: 0.9055 (ttmm) REVERT: S 73 ASP cc_start: 0.7295 (t70) cc_final: 0.7030 (t70) outliers start: 26 outliers final: 10 residues processed: 145 average time/residue: 0.7412 time to fit residues: 113.8643 Evaluate side-chains 138 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain C residue 1 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.062557 restraints weight = 19130.171| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.03 r_work: 0.2714 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10337 Z= 0.125 Angle : 0.571 9.200 14034 Z= 0.299 Chirality : 0.041 0.154 1574 Planarity : 0.004 0.038 1771 Dihedral : 4.801 46.487 1599 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.86 % Allowed : 14.60 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1259 helix: 2.87 (0.26), residues: 391 sheet: 0.74 (0.27), residues: 334 loop : -0.13 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.014 0.001 TYR S 190 PHE 0.023 0.001 PHE B 292 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00288 (10331) covalent geometry : angle 0.57066 (14024) SS BOND : bond 0.00431 ( 5) SS BOND : angle 0.94025 ( 10) hydrogen bonds : bond 0.03871 ( 488) hydrogen bonds : angle 4.02514 ( 1365) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.381 Fit side-chains REVERT: R 136 ASP cc_start: 0.8829 (t0) cc_final: 0.8533 (t0) REVERT: R 297 ASP cc_start: 0.7947 (t0) cc_final: 0.7322 (t0) REVERT: A 299 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8611 (mp0) REVERT: B 172 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7706 (pp20) REVERT: B 303 ASP cc_start: 0.8414 (m-30) cc_final: 0.8209 (m-30) REVERT: Y 32 LYS cc_start: 0.8554 (mtpm) cc_final: 0.7966 (mptm) REVERT: Y 36 ASP cc_start: 0.8425 (m-30) cc_final: 0.8155 (m-30) REVERT: Y 58 GLU cc_start: 0.8445 (pm20) cc_final: 0.7833 (pm20) REVERT: Y 63 GLU cc_start: 0.7843 (tt0) cc_final: 0.6206 (tm-30) REVERT: N 73 ASP cc_start: 0.8271 (t0) cc_final: 0.7679 (t0) REVERT: N 76 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9068 (ttmm) REVERT: N 106 ASP cc_start: 0.8612 (p0) cc_final: 0.8323 (p0) REVERT: N 107 CYS cc_start: 0.8818 (p) cc_final: 0.8558 (m) REVERT: S 73 ASP cc_start: 0.7228 (t70) cc_final: 0.6907 (t70) REVERT: S 89 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8111 (pp20) REVERT: S 220 GLU cc_start: 0.7178 (mp0) cc_final: 0.6940 (mp0) outliers start: 20 outliers final: 7 residues processed: 146 average time/residue: 0.7206 time to fit residues: 111.4743 Evaluate side-chains 141 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain C residue 1 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062790 restraints weight = 19191.712| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.04 r_work: 0.2719 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10337 Z= 0.125 Angle : 0.578 9.256 14034 Z= 0.299 Chirality : 0.041 0.149 1574 Planarity : 0.004 0.045 1771 Dihedral : 4.676 44.338 1599 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.95 % Allowed : 14.88 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1259 helix: 2.93 (0.26), residues: 391 sheet: 0.74 (0.27), residues: 334 loop : -0.11 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.014 0.001 TYR S 190 PHE 0.022 0.001 PHE B 292 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00291 (10331) covalent geometry : angle 0.57780 (14024) SS BOND : bond 0.00408 ( 5) SS BOND : angle 0.92987 ( 10) hydrogen bonds : bond 0.03828 ( 488) hydrogen bonds : angle 3.99362 ( 1365) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8830 (t0) cc_final: 0.8527 (t0) REVERT: R 297 ASP cc_start: 0.7943 (t0) cc_final: 0.7317 (t0) REVERT: A 299 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8605 (mp0) REVERT: B 172 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7699 (pp20) REVERT: B 303 ASP cc_start: 0.8384 (m-30) cc_final: 0.8159 (m-30) REVERT: Y 32 LYS cc_start: 0.8521 (mtpm) cc_final: 0.7967 (mptm) REVERT: Y 36 ASP cc_start: 0.8394 (m-30) cc_final: 0.8107 (m-30) REVERT: Y 58 GLU cc_start: 0.8433 (pm20) cc_final: 0.7869 (pm20) REVERT: Y 63 GLU cc_start: 0.7812 (tt0) cc_final: 0.6169 (tm-30) REVERT: N 73 ASP cc_start: 0.8278 (t0) cc_final: 0.7684 (t0) REVERT: N 76 LYS cc_start: 0.9446 (ttmm) cc_final: 0.9059 (ttmm) REVERT: N 106 ASP cc_start: 0.8640 (p0) cc_final: 0.8391 (p0) REVERT: N 107 CYS cc_start: 0.8802 (p) cc_final: 0.8562 (m) REVERT: S 73 ASP cc_start: 0.7210 (t70) cc_final: 0.6920 (t70) REVERT: S 89 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8124 (pp20) REVERT: C 6 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7778 (t) outliers start: 21 outliers final: 9 residues processed: 144 average time/residue: 0.7503 time to fit residues: 114.5696 Evaluate side-chains 142 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain C residue 1 CYS Chi-restraints excluded: chain C residue 6 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062099 restraints weight = 19313.072| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.02 r_work: 0.2700 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10337 Z= 0.145 Angle : 0.602 9.953 14034 Z= 0.312 Chirality : 0.042 0.152 1574 Planarity : 0.004 0.034 1771 Dihedral : 4.692 43.313 1599 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.14 % Allowed : 15.16 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1259 helix: 2.95 (0.26), residues: 391 sheet: 0.72 (0.27), residues: 334 loop : -0.10 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.022 0.001 TYR A 63 PHE 0.022 0.001 PHE B 292 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00345 (10331) covalent geometry : angle 0.60177 (14024) SS BOND : bond 0.00469 ( 5) SS BOND : angle 0.97099 ( 10) hydrogen bonds : bond 0.04039 ( 488) hydrogen bonds : angle 4.04072 ( 1365) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.452 Fit side-chains REVERT: R 136 ASP cc_start: 0.8862 (t0) cc_final: 0.8564 (t0) REVERT: R 297 ASP cc_start: 0.8044 (t0) cc_final: 0.7370 (t0) REVERT: A 299 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8630 (mp0) REVERT: B 172 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: B 254 ASP cc_start: 0.8433 (t0) cc_final: 0.7571 (p0) REVERT: B 303 ASP cc_start: 0.8474 (m-30) cc_final: 0.8261 (m-30) REVERT: Y 32 LYS cc_start: 0.8558 (mtpm) cc_final: 0.7968 (mptm) REVERT: Y 36 ASP cc_start: 0.8459 (m-30) cc_final: 0.8182 (m-30) REVERT: Y 58 GLU cc_start: 0.8455 (pm20) cc_final: 0.8192 (pm20) REVERT: Y 63 GLU cc_start: 0.7819 (tt0) cc_final: 0.6175 (tm-30) REVERT: N 73 ASP cc_start: 0.8308 (t0) cc_final: 0.7704 (t0) REVERT: N 76 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9061 (ttmm) REVERT: N 106 ASP cc_start: 0.8682 (p0) cc_final: 0.8457 (p0) REVERT: N 107 CYS cc_start: 0.8836 (p) cc_final: 0.8610 (m) REVERT: S 7 SER cc_start: 0.9414 (t) cc_final: 0.9053 (p) REVERT: S 73 ASP cc_start: 0.7273 (t70) cc_final: 0.6957 (t70) REVERT: C 6 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7796 (t) outliers start: 23 outliers final: 10 residues processed: 142 average time/residue: 0.7095 time to fit residues: 106.7120 Evaluate side-chains 142 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain C residue 1 CYS Chi-restraints excluded: chain C residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.062365 restraints weight = 19028.055| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.00 r_work: 0.2706 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10337 Z= 0.144 Angle : 0.621 10.226 14034 Z= 0.321 Chirality : 0.042 0.149 1574 Planarity : 0.004 0.055 1771 Dihedral : 4.657 42.432 1599 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.02 % Allowed : 16.47 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1259 helix: 2.80 (0.26), residues: 397 sheet: 0.72 (0.27), residues: 334 loop : -0.14 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.015 0.001 TYR A 63 PHE 0.021 0.001 PHE B 292 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00344 (10331) covalent geometry : angle 0.62108 (14024) SS BOND : bond 0.00446 ( 5) SS BOND : angle 0.97864 ( 10) hydrogen bonds : bond 0.03972 ( 488) hydrogen bonds : angle 4.03124 ( 1365) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.391 Fit side-chains REVERT: R 136 ASP cc_start: 0.8862 (t0) cc_final: 0.8563 (t0) REVERT: R 297 ASP cc_start: 0.7948 (t0) cc_final: 0.7379 (t0) REVERT: A 299 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8632 (mp0) REVERT: B 172 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7700 (pp20) REVERT: B 303 ASP cc_start: 0.8433 (m-30) cc_final: 0.8213 (m-30) REVERT: Y 32 LYS cc_start: 0.8535 (mtpm) cc_final: 0.7951 (mptm) REVERT: Y 36 ASP cc_start: 0.8448 (m-30) cc_final: 0.8170 (m-30) REVERT: Y 58 GLU cc_start: 0.8449 (pm20) cc_final: 0.8198 (pm20) REVERT: Y 63 GLU cc_start: 0.7820 (tt0) cc_final: 0.6179 (tm-30) REVERT: N 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7698 (t0) REVERT: N 76 LYS cc_start: 0.9458 (ttmm) cc_final: 0.9067 (ttmm) REVERT: N 106 ASP cc_start: 0.8687 (p0) cc_final: 0.8456 (p0) REVERT: N 107 CYS cc_start: 0.8810 (p) cc_final: 0.8582 (m) REVERT: S 7 SER cc_start: 0.9405 (t) cc_final: 0.9041 (p) REVERT: S 73 ASP cc_start: 0.7272 (t70) cc_final: 0.6988 (t70) REVERT: C 6 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (t) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.7582 time to fit residues: 107.4550 Evaluate side-chains 138 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain C residue 1 CYS Chi-restraints excluded: chain C residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.0570 chunk 101 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065156 restraints weight = 19303.060| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.03 r_work: 0.2769 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10337 Z= 0.111 Angle : 0.592 10.189 14034 Z= 0.304 Chirality : 0.041 0.158 1574 Planarity : 0.004 0.057 1771 Dihedral : 4.394 42.156 1599 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.84 % Allowed : 16.37 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1259 helix: 3.06 (0.26), residues: 388 sheet: 0.87 (0.27), residues: 329 loop : -0.11 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.026 0.001 TYR A 63 PHE 0.019 0.001 PHE B 292 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00257 (10331) covalent geometry : angle 0.59171 (14024) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.74446 ( 10) hydrogen bonds : bond 0.03274 ( 488) hydrogen bonds : angle 3.91084 ( 1365) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.59 seconds wall clock time: 68 minutes 23.32 seconds (4103.32 seconds total)