Starting phenix.real_space_refine on Mon Jul 28 05:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dw9_30877/07_2025/7dw9_30877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dw9_30877/07_2025/7dw9_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_30877/07_2025/7dw9_30877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dw9_30877/07_2025/7dw9_30877.map" model { file = "/net/cci-nas-00/data/ceres_data/7dw9_30877/07_2025/7dw9_30877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dw9_30877/07_2025/7dw9_30877.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 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: 6.25, per 1000 atoms: 0.62 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 3.13 Time building geometry restraints manager: 3.00 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: 0.580 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 25.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- 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 (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: -0.01 (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 TRP 0.042 0.005 TRP S 47 HIS 0.013 0.003 HIS A 357 PHE 0.018 0.002 PHE B 235 TYR 0.027 0.005 TYR A 253 ARG 0.023 0.003 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.20350 ( 488) hydrogen bonds : angle 7.01243 ( 1365) SS BOND : bond 0.00924 ( 5) SS BOND : angle 1.52575 ( 10) covalent geometry : bond 0.00618 (10331) covalent geometry : angle 0.77103 (14024) 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 : 1.109 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: 1.6490 time to fit residues: 316.4948 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 : 1.050 ------------------------------------------------------------------------------- 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 104 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** B 91 HIS B 293 ASN N 3 GLN S 77 ASN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061256 restraints weight = 19164.621| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.05 r_work: 0.2677 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1839 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= 0.211 Angle : 0.664 7.611 14034 Z= 0.355 Chirality : 0.046 0.211 1574 Planarity : 0.005 0.034 1771 Dihedral : 5.801 48.301 1602 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 7.07 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.15 (0.23), residues: 1259 helix: 1.81 (0.25), residues: 397 sheet: 0.78 (0.27), residues: 337 loop : 0.03 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.009 0.002 HIS A 357 PHE 0.025 0.002 PHE B 292 TYR 0.020 0.002 TYR C 2 ARG 0.006 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 488) hydrogen bonds : angle 4.66754 ( 1365) SS BOND : bond 0.00708 ( 5) SS BOND : angle 1.40485 ( 10) covalent geometry : bond 0.00497 (10331) covalent geometry : angle 0.66290 (14024) Misc. bond : bond 0.00016 ( 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 163 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8808 (t0) cc_final: 0.8506 (t0) REVERT: R 297 ASP cc_start: 0.7735 (t0) cc_final: 0.7017 (t0) REVERT: R 313 LEU cc_start: 0.8122 (tp) cc_final: 0.7716 (tm) REVERT: A 299 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8718 (mp0) REVERT: B 172 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: B 215 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8525 (mm-30) REVERT: B 254 ASP cc_start: 0.8406 (t70) cc_final: 0.8194 (t0) REVERT: B 292 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8044 (p90) REVERT: Y 32 LYS cc_start: 0.8234 (mptm) cc_final: 0.8016 (mtpm) REVERT: Y 36 ASP cc_start: 0.8427 (m-30) cc_final: 0.8178 (m-30) REVERT: Y 58 GLU cc_start: 0.8344 (pm20) cc_final: 0.7690 (pm20) REVERT: Y 63 GLU cc_start: 0.7612 (tt0) cc_final: 0.5998 (tm-30) REVERT: N 46 GLU cc_start: 0.8649 (pt0) cc_final: 0.8431 (pt0) REVERT: N 73 ASP cc_start: 0.8193 (t0) cc_final: 0.7657 (t0) REVERT: N 76 LYS cc_start: 0.9333 (ttmm) cc_final: 0.9037 (ttmm) REVERT: S 73 ASP cc_start: 0.7200 (t70) cc_final: 0.5795 (t70) REVERT: S 76 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8684 (mtmm) REVERT: S 223 ASP cc_start: 0.8437 (m-30) cc_final: 0.8035 (m-30) REVERT: S 234 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8297 (pt0) outliers start: 16 outliers final: 2 residues processed: 152 average time/residue: 2.4288 time to fit residues: 390.4021 Evaluate side-chains 129 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 292 PHE 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 10 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** R 317 ASN A 220 HIS N 3 GLN N 84 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.063968 restraints weight = 19350.385| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.05 r_work: 0.2754 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2414 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= 0.125 Angle : 0.569 7.896 14034 Z= 0.300 Chirality : 0.042 0.175 1574 Planarity : 0.004 0.036 1771 Dihedral : 5.197 58.822 1599 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.86 % Allowed : 8.74 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.55 (0.24), residues: 1259 helix: 2.47 (0.26), residues: 397 sheet: 0.95 (0.27), residues: 334 loop : 0.01 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE B 292 TYR 0.015 0.001 TYR S 190 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 488) hydrogen bonds : angle 4.18874 ( 1365) SS BOND : bond 0.00482 ( 5) SS BOND : angle 1.08851 ( 10) covalent geometry : bond 0.00282 (10331) covalent geometry : angle 0.56838 (14024) Misc. bond : bond 0.00004 ( 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 162 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.111 Fit side-chains REVERT: R 136 ASP cc_start: 0.8865 (t0) cc_final: 0.8603 (t0) REVERT: R 212 MET cc_start: 0.8853 (mmp) cc_final: 0.8503 (mmp) REVERT: R 297 ASP cc_start: 0.7797 (t0) cc_final: 0.7197 (t0) REVERT: R 313 LEU cc_start: 0.8353 (tp) cc_final: 0.7810 (tm) REVERT: A 59 GLN cc_start: 0.8464 (pp30) cc_final: 0.8258 (pp30) REVERT: A 299 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8557 (mp0) REVERT: B 172 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: B 217 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: B 254 ASP cc_start: 0.8430 (t70) cc_final: 0.8103 (t70) REVERT: Y 32 LYS cc_start: 0.8218 (mptm) cc_final: 0.7935 (mtpp) REVERT: Y 36 ASP cc_start: 0.8484 (m-30) cc_final: 0.8162 (m-30) REVERT: Y 58 GLU cc_start: 0.8361 (pm20) cc_final: 0.8057 (pm20) REVERT: Y 63 GLU cc_start: 0.7630 (tt0) cc_final: 0.6033 (tm-30) REVERT: N 43 LYS cc_start: 0.7201 (ptmm) cc_final: 0.6926 (pptt) REVERT: N 46 GLU cc_start: 0.8620 (pt0) cc_final: 0.8389 (pt0) REVERT: N 73 ASP cc_start: 0.8231 (t0) cc_final: 0.7644 (t0) REVERT: N 76 LYS cc_start: 0.9388 (ttmm) cc_final: 0.9016 (ttmm) REVERT: S 46 GLU cc_start: 0.8595 (tt0) cc_final: 0.8390 (tt0) REVERT: S 73 ASP cc_start: 0.7180 (t70) cc_final: 0.5729 (t70) REVERT: S 76 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8725 (mtmm) REVERT: S 219 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8249 (tp) REVERT: S 223 ASP cc_start: 0.8276 (m-30) cc_final: 0.7494 (m-30) outliers start: 20 outliers final: 4 residues processed: 150 average time/residue: 1.4949 time to fit residues: 237.9840 Evaluate side-chains 134 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET 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 S residue 219 LEU Chi-restraints excluded: chain C residue 1 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 12 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- 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** N 31 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.060513 restraints weight = 19276.850| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.01 r_work: 0.2659 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10337 Z= 0.227 Angle : 0.625 7.677 14034 Z= 0.330 Chirality : 0.045 0.196 1574 Planarity : 0.004 0.033 1771 Dihedral : 5.341 59.428 1599 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.86 % Allowed : 10.88 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.24), residues: 1259 helix: 2.53 (0.26), residues: 397 sheet: 0.82 (0.27), residues: 334 loop : -0.08 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.002 HIS A 357 PHE 0.022 0.002 PHE B 292 TYR 0.018 0.002 TYR B 105 ARG 0.008 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 488) hydrogen bonds : angle 4.29670 ( 1365) SS BOND : bond 0.00649 ( 5) SS BOND : angle 1.25694 ( 10) covalent geometry : bond 0.00540 (10331) covalent geometry : angle 0.62465 (14024) Misc. bond : bond 0.00002 ( 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 149 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.051 Fit side-chains REVERT: R 136 ASP cc_start: 0.8869 (t0) cc_final: 0.8593 (t0) REVERT: R 297 ASP cc_start: 0.7815 (t0) cc_final: 0.7210 (t0) REVERT: A 63 TYR cc_start: 0.7332 (m-10) cc_final: 0.7080 (m-10) REVERT: A 299 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8612 (mp0) REVERT: B 172 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: B 215 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 217 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8157 (pmm) REVERT: B 254 ASP cc_start: 0.8476 (t70) cc_final: 0.8129 (t70) REVERT: Y 32 LYS cc_start: 0.8266 (mptm) cc_final: 0.7974 (mtpm) REVERT: Y 36 ASP cc_start: 0.8500 (m-30) cc_final: 0.8237 (m-30) REVERT: Y 58 GLU cc_start: 0.8404 (pm20) cc_final: 0.8084 (pm20) REVERT: Y 63 GLU cc_start: 0.7649 (tt0) cc_final: 0.6097 (tm-30) REVERT: N 43 LYS cc_start: 0.7223 (ptmm) cc_final: 0.6967 (pptt) REVERT: N 46 GLU cc_start: 0.8660 (pt0) cc_final: 0.8454 (pt0) REVERT: N 73 ASP cc_start: 0.8285 (t0) cc_final: 0.7659 (t0) REVERT: N 76 LYS cc_start: 0.9424 (ttmm) cc_final: 0.9056 (ttmm) REVERT: S 46 GLU cc_start: 0.8617 (tt0) cc_final: 0.8405 (tt0) outliers start: 20 outliers final: 7 residues processed: 141 average time/residue: 1.5754 time to fit residues: 235.2494 Evaluate side-chains 134 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 217 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 C residue 1 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061364 restraints weight = 19295.184| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.02 r_work: 0.2680 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10337 Z= 0.165 Angle : 0.586 8.479 14034 Z= 0.308 Chirality : 0.043 0.178 1574 Planarity : 0.004 0.031 1771 Dihedral : 5.114 56.261 1599 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.14 % Allowed : 12.09 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.53 (0.24), residues: 1259 helix: 2.65 (0.26), residues: 397 sheet: 0.81 (0.27), residues: 334 loop : -0.08 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE B 292 TYR 0.015 0.001 TYR R 117 ARG 0.007 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 488) hydrogen bonds : angle 4.15715 ( 1365) SS BOND : bond 0.00546 ( 5) SS BOND : angle 1.08708 ( 10) covalent geometry : bond 0.00389 (10331) covalent geometry : angle 0.58595 (14024) Misc. bond : bond 0.00003 ( 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 156 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.189 Fit side-chains REVERT: R 136 ASP cc_start: 0.8864 (t0) cc_final: 0.8575 (t0) REVERT: R 297 ASP cc_start: 0.7890 (t0) cc_final: 0.7232 (t0) REVERT: A 299 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8617 (mp0) REVERT: B 172 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7737 (pp20) REVERT: B 254 ASP cc_start: 0.8464 (t70) cc_final: 0.8085 (t70) REVERT: B 262 MET cc_start: 0.8877 (ttm) cc_final: 0.8486 (ttm) REVERT: Y 32 LYS cc_start: 0.8331 (mptm) cc_final: 0.8032 (mtpm) REVERT: Y 36 ASP cc_start: 0.8495 (m-30) cc_final: 0.8219 (m-30) REVERT: Y 58 GLU cc_start: 0.8401 (pm20) cc_final: 0.8104 (pm20) REVERT: Y 63 GLU cc_start: 0.7719 (tt0) cc_final: 0.6164 (tm-30) REVERT: N 43 LYS cc_start: 0.7201 (ptmm) cc_final: 0.6968 (pptt) REVERT: N 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7669 (t0) REVERT: N 76 LYS cc_start: 0.9431 (ttmm) cc_final: 0.9060 (ttmm) REVERT: S 46 GLU cc_start: 0.8556 (tt0) cc_final: 0.8341 (tt0) REVERT: S 73 ASP cc_start: 0.7285 (t70) cc_final: 0.6806 (t70) REVERT: S 76 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9108 (mptt) outliers start: 23 outliers final: 8 residues processed: 144 average time/residue: 1.5493 time to fit residues: 236.2826 Evaluate side-chains 139 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 76 LYS 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 59 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 0.0970 overall best weight: 3.5784 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.095119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061365 restraints weight = 19459.093| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.04 r_work: 0.2682 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10337 Z= 0.160 Angle : 0.584 8.631 14034 Z= 0.306 Chirality : 0.043 0.172 1574 Planarity : 0.004 0.036 1771 Dihedral : 4.986 52.466 1599 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.33 % Allowed : 12.93 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.55 (0.24), residues: 1259 helix: 2.70 (0.26), residues: 398 sheet: 0.80 (0.27), residues: 334 loop : -0.10 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.014 0.001 TYR R 117 ARG 0.009 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 488) hydrogen bonds : angle 4.10998 ( 1365) SS BOND : bond 0.00519 ( 5) SS BOND : angle 1.03701 ( 10) covalent geometry : bond 0.00379 (10331) covalent geometry : angle 0.58314 (14024) Misc. bond : bond 0.00002 ( 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 157 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.101 Fit side-chains REVERT: R 136 ASP cc_start: 0.8865 (t0) cc_final: 0.8580 (t0) REVERT: R 297 ASP cc_start: 0.7903 (t0) cc_final: 0.7244 (t0) REVERT: A 299 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8628 (mp0) REVERT: B 172 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: B 254 ASP cc_start: 0.8483 (t70) cc_final: 0.8091 (t70) REVERT: B 303 ASP cc_start: 0.8513 (m-30) cc_final: 0.8294 (m-30) REVERT: Y 32 LYS cc_start: 0.8328 (mptm) cc_final: 0.8105 (mptm) REVERT: Y 36 ASP cc_start: 0.8500 (m-30) cc_final: 0.8215 (m-30) REVERT: Y 58 GLU cc_start: 0.8438 (pm20) cc_final: 0.8146 (pm20) REVERT: Y 63 GLU cc_start: 0.7785 (tt0) cc_final: 0.6217 (tm-30) REVERT: N 43 LYS cc_start: 0.7287 (ptmm) cc_final: 0.6877 (pptt) REVERT: N 73 ASP cc_start: 0.8302 (t0) cc_final: 0.7685 (t0) REVERT: N 76 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9093 (ttmm) REVERT: N 106 ASP cc_start: 0.8705 (p0) cc_final: 0.8409 (p0) REVERT: N 107 CYS cc_start: 0.8914 (p) cc_final: 0.8543 (m) REVERT: S 46 GLU cc_start: 0.8548 (tt0) cc_final: 0.8309 (tt0) REVERT: S 73 ASP cc_start: 0.7272 (t70) cc_final: 0.6942 (t70) REVERT: S 76 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9223 (mttp) outliers start: 25 outliers final: 10 residues processed: 145 average time/residue: 1.5342 time to fit residues: 235.8385 Evaluate side-chains 141 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 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 S residue 76 LYS 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 108 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.063503 restraints weight = 19417.476| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.05 r_work: 0.2731 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3036 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= 0.114 Angle : 0.554 9.268 14034 Z= 0.288 Chirality : 0.041 0.151 1574 Planarity : 0.004 0.038 1771 Dihedral : 4.645 47.574 1599 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.58 % Allowed : 14.23 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.74 (0.24), residues: 1259 helix: 2.97 (0.26), residues: 391 sheet: 0.98 (0.27), residues: 323 loop : -0.06 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 150 PHE 0.013 0.001 PHE B 292 TYR 0.014 0.001 TYR S 190 ARG 0.009 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 488) hydrogen bonds : angle 3.94452 ( 1365) SS BOND : bond 0.00365 ( 5) SS BOND : angle 0.84183 ( 10) covalent geometry : bond 0.00259 (10331) covalent geometry : angle 0.55330 (14024) 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 160 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.211 Fit side-chains REVERT: R 136 ASP cc_start: 0.8853 (t0) cc_final: 0.8517 (t0) REVERT: R 297 ASP cc_start: 0.7979 (t0) cc_final: 0.7259 (t0) REVERT: A 299 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8582 (mp0) REVERT: B 172 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7737 (pp20) REVERT: B 254 ASP cc_start: 0.8435 (t70) cc_final: 0.8030 (t70) REVERT: B 303 ASP cc_start: 0.8406 (m-30) cc_final: 0.8182 (m-30) REVERT: Y 32 LYS cc_start: 0.8306 (mptm) cc_final: 0.8093 (mptm) REVERT: Y 36 ASP cc_start: 0.8476 (m-30) cc_final: 0.8177 (m-30) REVERT: Y 58 GLU cc_start: 0.8426 (pm20) cc_final: 0.7772 (pm20) REVERT: Y 63 GLU cc_start: 0.7746 (tt0) cc_final: 0.6108 (tm-30) REVERT: N 73 ASP cc_start: 0.8267 (t0) cc_final: 0.7677 (t0) REVERT: N 76 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9097 (ttmm) REVERT: N 106 ASP cc_start: 0.8684 (p0) cc_final: 0.8468 (p0) REVERT: N 107 CYS cc_start: 0.8787 (p) cc_final: 0.8568 (m) REVERT: S 46 GLU cc_start: 0.8488 (tt0) cc_final: 0.8263 (tt0) REVERT: S 73 ASP cc_start: 0.7233 (t70) cc_final: 0.6932 (t70) REVERT: S 89 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: C 6 CYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7661 (t) outliers start: 17 outliers final: 7 residues processed: 151 average time/residue: 1.5532 time to fit residues: 248.9408 Evaluate side-chains 145 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 THR 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 6 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 50.0000 chunk 112 optimal weight: 0.0470 chunk 68 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 0.0170 overall best weight: 1.2318 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.064515 restraints weight = 19460.429| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.06 r_work: 0.2755 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10337 Z= 0.107 Angle : 0.562 9.387 14034 Z= 0.290 Chirality : 0.040 0.140 1574 Planarity : 0.004 0.039 1771 Dihedral : 4.454 45.563 1599 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.12 % Allowed : 15.81 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1259 helix: 3.05 (0.26), residues: 390 sheet: 0.97 (0.27), residues: 322 loop : -0.07 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR S 190 ARG 0.010 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 488) hydrogen bonds : angle 3.86940 ( 1365) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.72358 ( 10) covalent geometry : bond 0.00245 (10331) covalent geometry : angle 0.56143 (14024) Misc. bond : bond 0.00002 ( 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 164 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.057 Fit side-chains REVERT: R 136 ASP cc_start: 0.8863 (t0) cc_final: 0.8537 (t0) REVERT: R 297 ASP cc_start: 0.7958 (t0) cc_final: 0.7274 (t0) REVERT: A 63 TYR cc_start: 0.7461 (m-10) cc_final: 0.7217 (m-10) REVERT: A 299 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8578 (mp0) REVERT: B 172 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7699 (pp20) REVERT: B 254 ASP cc_start: 0.8444 (t70) cc_final: 0.8046 (t70) REVERT: B 303 ASP cc_start: 0.8369 (m-30) cc_final: 0.8148 (m-30) REVERT: Y 32 LYS cc_start: 0.8318 (mptm) cc_final: 0.8111 (mptm) REVERT: Y 36 ASP cc_start: 0.8482 (m-30) cc_final: 0.8168 (m-30) REVERT: Y 58 GLU cc_start: 0.8413 (pm20) cc_final: 0.7826 (pm20) REVERT: Y 63 GLU cc_start: 0.7760 (tt0) cc_final: 0.6096 (tm-30) REVERT: N 73 ASP cc_start: 0.8234 (t0) cc_final: 0.7647 (t0) REVERT: N 76 LYS cc_start: 0.9457 (ttmm) cc_final: 0.9106 (ttmm) REVERT: S 7 SER cc_start: 0.9388 (t) cc_final: 0.9030 (p) REVERT: S 46 GLU cc_start: 0.8466 (tt0) cc_final: 0.8212 (tt0) REVERT: S 73 ASP cc_start: 0.6984 (t70) cc_final: 0.6527 (t0) REVERT: S 76 LYS cc_start: 0.9424 (mttp) cc_final: 0.9188 (mmtm) REVERT: C 6 CYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7574 (t) outliers start: 12 outliers final: 6 residues processed: 158 average time/residue: 1.4892 time to fit residues: 250.1326 Evaluate side-chains 145 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 120 GLN 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 113 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 116 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 0.0020 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 overall best weight: 2.1750 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.063448 restraints weight = 19450.856| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.05 r_work: 0.2732 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3196 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= 0.127 Angle : 0.597 9.359 14034 Z= 0.307 Chirality : 0.041 0.146 1574 Planarity : 0.004 0.044 1771 Dihedral : 4.504 45.389 1599 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.58 % Allowed : 15.35 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.24), residues: 1259 helix: 2.85 (0.26), residues: 397 sheet: 0.98 (0.27), residues: 323 loop : -0.13 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 PHE 0.012 0.001 PHE B 292 TYR 0.013 0.001 TYR R 117 ARG 0.011 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 488) hydrogen bonds : angle 3.91571 ( 1365) SS BOND : bond 0.00400 ( 5) SS BOND : angle 0.89381 ( 10) covalent geometry : bond 0.00303 (10331) covalent geometry : angle 0.59627 (14024) 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 153 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8864 (t0) cc_final: 0.8578 (t0) REVERT: R 297 ASP cc_start: 0.7955 (t0) cc_final: 0.7240 (t0) REVERT: A 63 TYR cc_start: 0.7472 (m-10) cc_final: 0.7252 (m-10) REVERT: A 299 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8605 (mp0) REVERT: B 172 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7703 (pp20) REVERT: B 254 ASP cc_start: 0.8450 (t70) cc_final: 0.8048 (t70) REVERT: B 303 ASP cc_start: 0.8375 (m-30) cc_final: 0.8164 (m-30) REVERT: Y 32 LYS cc_start: 0.8338 (mptm) cc_final: 0.8124 (mptm) REVERT: Y 36 ASP cc_start: 0.8479 (m-30) cc_final: 0.8167 (m-30) REVERT: Y 58 GLU cc_start: 0.8419 (pm20) cc_final: 0.7824 (pm20) REVERT: Y 63 GLU cc_start: 0.7825 (tt0) cc_final: 0.6142 (tm-30) REVERT: N 73 ASP cc_start: 0.8259 (t0) cc_final: 0.7662 (t0) REVERT: N 76 LYS cc_start: 0.9459 (ttmm) cc_final: 0.9107 (ttmm) REVERT: S 7 SER cc_start: 0.9391 (t) cc_final: 0.9029 (p) REVERT: S 46 GLU cc_start: 0.8510 (tt0) cc_final: 0.8251 (tt0) REVERT: S 73 ASP cc_start: 0.7042 (t70) cc_final: 0.6572 (t0) REVERT: S 76 LYS cc_start: 0.9415 (mttp) cc_final: 0.9189 (mmtm) REVERT: S 192 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8960 (ttp) REVERT: C 6 CYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7610 (t) outliers start: 17 outliers final: 8 residues processed: 145 average time/residue: 1.5595 time to fit residues: 239.5643 Evaluate side-chains 146 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 THR 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 3 GLN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 192 MET 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 108 optimal weight: 10.0000 chunk 46 optimal weight: 0.0060 chunk 91 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.095358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.061497 restraints weight = 19400.893| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.05 r_work: 0.2687 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10337 Z= 0.170 Angle : 0.635 9.431 14034 Z= 0.330 Chirality : 0.043 0.163 1574 Planarity : 0.004 0.038 1771 Dihedral : 4.742 44.623 1599 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.40 % Allowed : 15.53 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.24), residues: 1259 helix: 2.77 (0.26), residues: 399 sheet: 0.83 (0.27), residues: 334 loop : -0.13 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS R 150 PHE 0.015 0.002 PHE B 292 TYR 0.014 0.001 TYR R 117 ARG 0.012 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 488) hydrogen bonds : angle 4.08697 ( 1365) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.06827 ( 10) covalent geometry : bond 0.00409 (10331) covalent geometry : angle 0.63445 (14024) Misc. bond : bond 0.00002 ( 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 152 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.169 Fit side-chains REVERT: R 136 ASP cc_start: 0.8867 (t0) cc_final: 0.8564 (t0) REVERT: R 297 ASP cc_start: 0.7992 (t0) cc_final: 0.7336 (t0) REVERT: A 63 TYR cc_start: 0.7498 (m-10) cc_final: 0.7250 (m-10) REVERT: A 299 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8620 (mp0) REVERT: B 172 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7704 (pp20) REVERT: B 254 ASP cc_start: 0.8500 (t70) cc_final: 0.8113 (t70) REVERT: B 303 ASP cc_start: 0.8499 (m-30) cc_final: 0.8275 (m-30) REVERT: Y 32 LYS cc_start: 0.8344 (mptm) cc_final: 0.8131 (mptm) REVERT: Y 36 ASP cc_start: 0.8481 (m-30) cc_final: 0.8188 (m-30) REVERT: Y 58 GLU cc_start: 0.8432 (pm20) cc_final: 0.7790 (pm20) REVERT: Y 63 GLU cc_start: 0.7844 (tt0) cc_final: 0.6175 (tm-30) REVERT: N 73 ASP cc_start: 0.8322 (t0) cc_final: 0.7688 (t0) REVERT: N 76 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9067 (ttmm) REVERT: S 7 SER cc_start: 0.9426 (t) cc_final: 0.9058 (p) REVERT: S 43 LYS cc_start: 0.9009 (mmpt) cc_final: 0.7239 (mmpt) REVERT: S 46 GLU cc_start: 0.8599 (tt0) cc_final: 0.8325 (tt0) REVERT: S 73 ASP cc_start: 0.7088 (t70) cc_final: 0.6866 (t70) REVERT: C 6 CYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7778 (t) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 1.5596 time to fit residues: 234.5147 Evaluate side-chains 149 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 272 MET 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 57 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 192 MET 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 4 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 116 optimal weight: 0.0050 chunk 35 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 67 optimal weight: 0.0670 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.098599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065001 restraints weight = 19273.966| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.05 r_work: 0.2765 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3365 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= 0.114 Angle : 0.606 10.166 14034 Z= 0.311 Chirality : 0.041 0.159 1574 Planarity : 0.004 0.046 1771 Dihedral : 4.467 42.564 1599 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.21 % Allowed : 16.37 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.75 (0.24), residues: 1259 helix: 3.06 (0.26), residues: 388 sheet: 1.03 (0.27), residues: 323 loop : -0.14 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.020 0.001 PHE N 108 TYR 0.014 0.001 TYR S 190 ARG 0.012 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 488) hydrogen bonds : angle 3.91746 ( 1365) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.74684 ( 10) covalent geometry : bond 0.00255 (10331) covalent geometry : angle 0.60589 (14024) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9066.81 seconds wall clock time: 159 minutes 26.17 seconds (9566.17 seconds total)