Starting phenix.real_space_refine on Fri Feb 14 09:44:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dw9_30877/02_2025/7dw9_30877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dw9_30877/02_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_30877/02_2025/7dw9_30877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dw9_30877/02_2025/7dw9_30877.map" model { file = "/net/cci-nas-00/data/ceres_data/7dw9_30877/02_2025/7dw9_30877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dw9_30877/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.57, per 1000 atoms: 0.55 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: 2.73 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: 0.93 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: 2.64 Time building geometry restraints manager: 3.10 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- 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 0.052 10331 Z= 0.404 Angle : 0.771 12.081 14024 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 *********************** 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 : 1.083 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: 1.7216 time to fit residues: 330.0018 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 : 1.240 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061254 restraints weight = 19164.619| |-----------------------------------------------------------------------------| 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: 0.8433 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 10331 Z= 0.324 Angle : 0.663 7.611 14024 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 *********************** 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 : 1.244 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8810 (t0) cc_final: 0.8507 (t0) REVERT: R 297 ASP cc_start: 0.7737 (t0) cc_final: 0.7019 (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: 0.8811 (mm-30) cc_final: 0.8527 (mm-30) REVERT: B 254 ASP cc_start: 0.8406 (t70) cc_final: 0.8195 (t0) REVERT: B 292 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8046 (p90) REVERT: Y 32 LYS cc_start: 0.8235 (mptm) cc_final: 0.8016 (mtpm) REVERT: Y 36 ASP cc_start: 0.8427 (m-30) cc_final: 0.8179 (m-30) REVERT: Y 58 GLU cc_start: 0.8346 (pm20) cc_final: 0.7692 (pm20) REVERT: Y 63 GLU cc_start: 0.7613 (tt0) cc_final: 0.5999 (tm-30) REVERT: N 46 GLU cc_start: 0.8650 (pt0) cc_final: 0.8433 (pt0) REVERT: N 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7659 (t0) REVERT: N 76 LYS cc_start: 0.9334 (ttmm) cc_final: 0.9038 (ttmm) REVERT: S 73 ASP cc_start: 0.7201 (t70) cc_final: 0.5796 (t70) REVERT: S 76 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8685 (mtmm) REVERT: S 223 ASP cc_start: 0.8438 (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: 1.6156 time to fit residues: 260.4921 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 : 1.092 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.097591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063701 restraints weight = 19367.312| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.06 r_work: 0.2748 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10331 Z= 0.191 Angle : 0.572 7.829 14024 Z= 0.301 Chirality : 0.042 0.175 1574 Planarity : 0.004 0.039 1771 Dihedral : 5.225 58.465 1599 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.86 % Allowed : 8.93 % Favored : 89.21 % 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: 1.54 (0.24), residues: 1259 helix: 2.48 (0.26), residues: 396 sheet: 0.94 (0.27), residues: 334 loop : -0.00 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 *********************** 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 : 1.205 Fit side-chains REVERT: R 136 ASP cc_start: 0.8872 (t0) cc_final: 0.8610 (t0) REVERT: R 212 MET cc_start: 0.8855 (mmp) cc_final: 0.8498 (mmp) REVERT: R 297 ASP cc_start: 0.7796 (t0) cc_final: 0.7185 (t0) REVERT: R 313 LEU cc_start: 0.8362 (tp) cc_final: 0.7817 (tm) REVERT: A 59 GLN cc_start: 0.8468 (pp30) cc_final: 0.8191 (pp30) REVERT: A 299 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8565 (mp0) REVERT: B 172 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: B 217 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8110 (pmm) REVERT: B 254 ASP cc_start: 0.8440 (t70) cc_final: 0.8119 (t70) REVERT: Y 32 LYS cc_start: 0.8221 (mptm) cc_final: 0.7942 (mtpm) REVERT: Y 36 ASP cc_start: 0.8486 (m-30) cc_final: 0.8182 (m-30) REVERT: Y 58 GLU cc_start: 0.8365 (pm20) cc_final: 0.8059 (pm20) REVERT: Y 63 GLU cc_start: 0.7631 (tt0) cc_final: 0.6035 (tm-30) REVERT: N 43 LYS cc_start: 0.7203 (ptmm) cc_final: 0.6926 (pptt) REVERT: N 46 GLU cc_start: 0.8624 (pt0) cc_final: 0.8391 (pt0) REVERT: N 73 ASP cc_start: 0.8235 (t0) cc_final: 0.7644 (t0) REVERT: N 76 LYS cc_start: 0.9388 (ttmm) cc_final: 0.9015 (ttmm) REVERT: S 73 ASP cc_start: 0.7178 (t70) cc_final: 0.5725 (t70) REVERT: S 76 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8723 (mtmm) REVERT: S 219 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8253 (tp) REVERT: S 223 ASP cc_start: 0.8281 (m-30) cc_final: 0.7458 (m-30) REVERT: S 234 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8430 (pt0) outliers start: 20 outliers final: 4 residues processed: 150 average time/residue: 1.5609 time to fit residues: 248.5133 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 : 1.123 ------------------------------------------------------------------------------- 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: 7.9990 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3453 r_free = 0.3453 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060039 restraints weight = 19301.759| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.00 r_work: 0.2649 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10331 Z= 0.388 Angle : 0.643 7.559 14024 Z= 0.340 Chirality : 0.045 0.201 1574 Planarity : 0.005 0.034 1771 Dihedral : 5.430 59.277 1599 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 10.79 % 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: 1.41 (0.24), residues: 1259 helix: 2.48 (0.26), residues: 397 sheet: 0.78 (0.27), residues: 339 loop : -0.13 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.022 0.002 PHE B 292 TYR 0.020 0.002 TYR B 105 ARG 0.008 0.001 ARG A 317 *********************** 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 151 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.109 Fit side-chains REVERT: R 136 ASP cc_start: 0.8866 (t0) cc_final: 0.8582 (t0) REVERT: R 297 ASP cc_start: 0.7819 (t0) cc_final: 0.7266 (t0) REVERT: A 63 TYR cc_start: 0.7302 (m-10) cc_final: 0.7061 (m-10) REVERT: A 299 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8622 (mp0) REVERT: B 172 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: B 215 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 217 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8165 (pmm) REVERT: B 254 ASP cc_start: 0.8498 (t70) cc_final: 0.8156 (t70) REVERT: Y 32 LYS cc_start: 0.8282 (mptm) cc_final: 0.7995 (mtpm) REVERT: Y 36 ASP cc_start: 0.8520 (m-30) cc_final: 0.8249 (m-30) REVERT: Y 58 GLU cc_start: 0.8405 (pm20) cc_final: 0.8082 (pm20) REVERT: Y 63 GLU cc_start: 0.7764 (tt0) cc_final: 0.6180 (tm-30) REVERT: N 43 LYS cc_start: 0.7281 (ptmm) cc_final: 0.7028 (pptt) REVERT: N 73 ASP cc_start: 0.8291 (t0) cc_final: 0.7648 (t0) REVERT: N 76 LYS cc_start: 0.9427 (ttmm) cc_final: 0.9055 (ttmm) outliers start: 21 outliers final: 7 residues processed: 141 average time/residue: 1.6261 time to fit residues: 242.7802 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 : 1.260 ------------------------------------------------------------------------------- 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: 8.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 106 optimal weight: 0.0270 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.096051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.062375 restraints weight = 19235.161| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.03 r_work: 0.2703 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10331 Z= 0.197 Angle : 0.565 8.697 14024 Z= 0.296 Chirality : 0.042 0.168 1574 Planarity : 0.004 0.030 1771 Dihedral : 5.001 55.083 1599 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.95 % Allowed : 12.56 % Favored : 85.49 % 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: 1.57 (0.24), residues: 1259 helix: 2.70 (0.26), residues: 398 sheet: 0.82 (0.27), residues: 334 loop : -0.06 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.015 0.001 TYR S 190 ARG 0.006 0.000 ARG A 317 *********************** 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 158 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.250 Fit side-chains REVERT: R 136 ASP cc_start: 0.8861 (t0) cc_final: 0.8575 (t0) REVERT: R 297 ASP cc_start: 0.7860 (t0) cc_final: 0.7209 (t0) REVERT: A 299 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8611 (mp0) REVERT: B 172 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7768 (pp20) REVERT: B 254 ASP cc_start: 0.8438 (t70) cc_final: 0.8048 (t70) REVERT: B 262 MET cc_start: 0.8858 (ttm) cc_final: 0.8472 (ttm) REVERT: B 303 ASP cc_start: 0.8504 (m-30) cc_final: 0.8301 (m-30) REVERT: Y 32 LYS cc_start: 0.8311 (mptm) cc_final: 0.8087 (mptm) REVERT: Y 36 ASP cc_start: 0.8504 (m-30) cc_final: 0.8221 (m-30) REVERT: Y 58 GLU cc_start: 0.8391 (pm20) cc_final: 0.8093 (pm20) REVERT: Y 63 GLU cc_start: 0.7720 (tt0) cc_final: 0.6093 (tm-30) REVERT: N 43 LYS cc_start: 0.7192 (ptmm) cc_final: 0.6892 (pptt) REVERT: N 73 ASP cc_start: 0.8265 (t0) cc_final: 0.7665 (t0) REVERT: N 76 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9080 (ttmm) REVERT: S 73 ASP cc_start: 0.7273 (t70) cc_final: 0.6745 (t70) REVERT: S 76 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9107 (mptt) outliers start: 21 outliers final: 8 residues processed: 148 average time/residue: 1.5307 time to fit residues: 240.5326 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 : 1.220 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.093618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059982 restraints weight = 19335.441| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.03 r_work: 0.2654 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10331 Z= 0.379 Angle : 0.644 8.233 14024 Z= 0.337 Chirality : 0.045 0.191 1574 Planarity : 0.004 0.034 1771 Dihedral : 5.216 53.030 1599 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.05 % Allowed : 13.30 % Favored : 84.65 % 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: 1.42 (0.24), residues: 1259 helix: 2.59 (0.26), residues: 397 sheet: 0.76 (0.27), residues: 332 loop : -0.18 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE B 292 TYR 0.016 0.002 TYR R 117 ARG 0.009 0.001 ARG A 317 *********************** 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: 22 poor density : 135 time to evaluate : 1.103 Fit side-chains REVERT: R 136 ASP cc_start: 0.8842 (t0) cc_final: 0.8564 (t0) REVERT: R 297 ASP cc_start: 0.7878 (t0) cc_final: 0.7229 (t0) REVERT: A 299 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8607 (mp0) REVERT: B 172 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: B 254 ASP cc_start: 0.8495 (t70) cc_final: 0.8128 (t70) REVERT: B 262 MET cc_start: 0.8898 (ttm) cc_final: 0.8562 (tpp) REVERT: B 303 ASP cc_start: 0.8553 (m-30) cc_final: 0.8335 (m-30) REVERT: Y 32 LYS cc_start: 0.8305 (mptm) cc_final: 0.7990 (mtpm) REVERT: Y 36 ASP cc_start: 0.8491 (m-30) cc_final: 0.8221 (m-30) REVERT: Y 58 GLU cc_start: 0.8436 (pm20) cc_final: 0.8141 (pm20) REVERT: Y 63 GLU cc_start: 0.7822 (tt0) cc_final: 0.6208 (tm-30) REVERT: N 43 LYS cc_start: 0.7271 (ptmm) cc_final: 0.6786 (pptt) REVERT: N 73 ASP cc_start: 0.8307 (t0) cc_final: 0.7664 (t0) REVERT: N 76 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9073 (ttmm) REVERT: N 106 ASP cc_start: 0.8681 (p0) cc_final: 0.8346 (p0) REVERT: N 107 CYS cc_start: 0.8970 (p) cc_final: 0.8395 (m) REVERT: S 73 ASP cc_start: 0.7222 (t70) cc_final: 0.5723 (t70) REVERT: S 76 LYS cc_start: 0.9414 (mtmm) cc_final: 0.8885 (mtmm) outliers start: 22 outliers final: 10 residues processed: 148 average time/residue: 1.5639 time to fit residues: 245.5220 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 : 1.215 ------------------------------------------------------------------------------- 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 C residue 1 CYS Chi-restraints excluded: chain C residue 6 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 59 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.097413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.063755 restraints weight = 19449.075| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.06 r_work: 0.2738 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10331 Z= 0.150 Angle : 0.559 9.518 14024 Z= 0.291 Chirality : 0.041 0.147 1574 Planarity : 0.004 0.035 1771 Dihedral : 4.712 47.060 1599 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.02 % Allowed : 14.98 % Favored : 84.00 % 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: 1.64 (0.24), residues: 1259 helix: 2.90 (0.26), residues: 392 sheet: 0.81 (0.27), residues: 334 loop : -0.07 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 292 TYR 0.015 0.001 TYR S 190 ARG 0.007 0.000 ARG S 160 *********************** 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: 11 poor density : 147 time to evaluate : 1.080 Fit side-chains REVERT: R 136 ASP cc_start: 0.8845 (t0) cc_final: 0.8555 (t0) REVERT: R 297 ASP cc_start: 0.7976 (t0) cc_final: 0.7270 (t0) REVERT: A 299 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8600 (mp0) REVERT: B 172 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7749 (pp20) REVERT: B 254 ASP cc_start: 0.8455 (t70) cc_final: 0.8052 (t70) REVERT: B 303 ASP cc_start: 0.8424 (m-30) cc_final: 0.8211 (m-30) REVERT: Y 32 LYS cc_start: 0.8331 (mptm) cc_final: 0.8105 (mptm) REVERT: Y 36 ASP cc_start: 0.8542 (m-30) cc_final: 0.8229 (m-30) REVERT: Y 58 GLU cc_start: 0.8419 (pm20) cc_final: 0.7766 (pm20) REVERT: Y 63 GLU cc_start: 0.7727 (tt0) cc_final: 0.6091 (tm-30) REVERT: N 46 GLU cc_start: 0.8532 (pt0) cc_final: 0.8328 (pt0) REVERT: N 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7665 (t0) REVERT: N 76 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9089 (ttmm) REVERT: N 106 ASP cc_start: 0.8677 (p0) cc_final: 0.8456 (p0) REVERT: N 107 CYS cc_start: 0.8800 (p) cc_final: 0.8575 (m) REVERT: S 73 ASP cc_start: 0.7214 (t70) cc_final: 0.6747 (t70) REVERT: S 76 LYS cc_start: 0.9446 (mtmm) cc_final: 0.9130 (mptt) REVERT: S 192 MET cc_start: 0.8917 (ttp) cc_final: 0.8712 (ttm) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 1.5510 time to fit residues: 248.3030 Evaluate side-chains 141 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 120 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 0.0870 overall best weight: 2.5164 ------------------------------------------------------------------------------- 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 ** 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 = 0.3491 r_free = 0.3491 target = 0.096225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.062420 restraints weight = 19516.092| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.05 r_work: 0.2707 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10331 Z= 0.204 Angle : 0.592 9.618 14024 Z= 0.307 Chirality : 0.041 0.155 1574 Planarity : 0.004 0.045 1771 Dihedral : 4.679 46.080 1599 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.58 % Allowed : 15.16 % Favored : 83.26 % 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: 1.69 (0.24), residues: 1259 helix: 2.95 (0.26), residues: 392 sheet: 0.88 (0.27), residues: 332 loop : -0.07 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 PHE 0.013 0.001 PHE B 292 TYR 0.013 0.001 TYR R 117 ARG 0.010 0.000 ARG B 214 *********************** 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 154 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8860 (t0) cc_final: 0.8522 (t0) REVERT: R 297 ASP cc_start: 0.7981 (t0) cc_final: 0.7276 (t0) REVERT: A 299 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8621 (mp0) REVERT: B 172 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7721 (pp20) REVERT: B 254 ASP cc_start: 0.8487 (t70) cc_final: 0.8084 (t70) REVERT: B 303 ASP cc_start: 0.8419 (m-30) cc_final: 0.8208 (m-30) REVERT: Y 32 LYS cc_start: 0.8352 (mptm) cc_final: 0.8136 (mptm) REVERT: Y 36 ASP cc_start: 0.8544 (m-30) cc_final: 0.8245 (m-30) REVERT: Y 58 GLU cc_start: 0.8441 (pm20) cc_final: 0.7787 (pm20) REVERT: Y 63 GLU cc_start: 0.7815 (tt0) cc_final: 0.6168 (tm-30) REVERT: N 73 ASP cc_start: 0.8283 (t0) cc_final: 0.7691 (t0) REVERT: N 76 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9076 (ttmm) REVERT: N 106 ASP cc_start: 0.8678 (p0) cc_final: 0.8430 (p0) REVERT: N 107 CYS cc_start: 0.8828 (p) cc_final: 0.8561 (m) REVERT: S 73 ASP cc_start: 0.7210 (t70) cc_final: 0.5705 (t70) REVERT: S 76 LYS cc_start: 0.9447 (mtmm) cc_final: 0.8908 (mtmm) REVERT: C 6 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7716 (t) outliers start: 17 outliers final: 9 residues processed: 147 average time/residue: 1.5764 time to fit residues: 245.8037 Evaluate side-chains 145 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 3 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3513 r_free = 0.3513 target = 0.097564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064049 restraints weight = 19399.976| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.04 r_work: 0.2741 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10331 Z= 0.174 Angle : 0.589 9.502 14024 Z= 0.304 Chirality : 0.041 0.144 1574 Planarity : 0.004 0.041 1771 Dihedral : 4.522 44.319 1599 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 15.26 % Favored : 83.44 % 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: 1.74 (0.24), residues: 1259 helix: 3.00 (0.26), residues: 391 sheet: 0.94 (0.27), residues: 330 loop : -0.07 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 292 TYR 0.014 0.001 TYR S 190 ARG 0.011 0.000 ARG B 214 *********************** 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: 14 poor density : 139 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8847 (t0) cc_final: 0.8550 (t0) REVERT: R 297 ASP cc_start: 0.7975 (t0) cc_final: 0.7281 (t0) REVERT: A 299 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8589 (mp0) REVERT: B 172 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7700 (pp20) REVERT: B 217 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7789 (pmm) REVERT: B 254 ASP cc_start: 0.8459 (t70) cc_final: 0.8060 (t70) REVERT: B 303 ASP cc_start: 0.8382 (m-30) cc_final: 0.8165 (m-30) REVERT: Y 32 LYS cc_start: 0.8340 (mptm) cc_final: 0.8127 (mptm) REVERT: Y 36 ASP cc_start: 0.8504 (m-30) cc_final: 0.8188 (m-30) REVERT: Y 58 GLU cc_start: 0.8424 (pm20) cc_final: 0.7770 (pm20) REVERT: Y 63 GLU cc_start: 0.7809 (tt0) cc_final: 0.6162 (tm-30) REVERT: N 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7653 (t0) REVERT: N 76 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9093 (ttmm) REVERT: N 106 ASP cc_start: 0.8687 (p0) cc_final: 0.8468 (p0) REVERT: N 107 CYS cc_start: 0.8770 (p) cc_final: 0.8561 (m) REVERT: S 7 SER cc_start: 0.9395 (t) cc_final: 0.9007 (p) REVERT: S 43 LYS cc_start: 0.8861 (mppt) cc_final: 0.8559 (mmpt) REVERT: S 73 ASP cc_start: 0.7174 (t70) cc_final: 0.5707 (t70) REVERT: S 76 LYS cc_start: 0.9446 (mtmm) cc_final: 0.8912 (mtmm) REVERT: C 6 CYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7644 (t) outliers start: 14 outliers final: 7 residues processed: 145 average time/residue: 1.5589 time to fit residues: 239.9726 Evaluate side-chains 147 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 THR 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 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 108 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3496 r_free = 0.3496 target = 0.096453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062828 restraints weight = 19314.053| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.03 r_work: 0.2716 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10331 Z= 0.215 Angle : 0.606 10.343 14024 Z= 0.314 Chirality : 0.042 0.162 1574 Planarity : 0.004 0.040 1771 Dihedral : 4.585 44.065 1599 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.21 % Allowed : 15.26 % 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 (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: 1.63 (0.24), residues: 1259 helix: 2.85 (0.26), residues: 398 sheet: 0.85 (0.27), residues: 334 loop : -0.12 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 292 TYR 0.013 0.001 TYR R 117 ARG 0.013 0.000 ARG B 214 ********************** 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 151 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8848 (t0) cc_final: 0.8541 (t0) REVERT: R 297 ASP cc_start: 0.7905 (t0) cc_final: 0.7279 (t0) REVERT: A 299 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8597 (mp0) REVERT: B 52 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8492 (ptt180) REVERT: B 172 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7704 (pp20) REVERT: B 217 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7796 (pmm) REVERT: B 254 ASP cc_start: 0.8503 (t70) cc_final: 0.8114 (t70) REVERT: B 303 ASP cc_start: 0.8460 (m-30) cc_final: 0.8253 (m-30) REVERT: Y 32 LYS cc_start: 0.8368 (mptm) cc_final: 0.8161 (mptm) REVERT: Y 36 ASP cc_start: 0.8535 (m-30) cc_final: 0.8231 (m-30) REVERT: Y 58 GLU cc_start: 0.8434 (pm20) cc_final: 0.8157 (pm20) REVERT: Y 63 GLU cc_start: 0.7828 (tt0) cc_final: 0.6151 (tm-30) REVERT: N 73 ASP cc_start: 0.8293 (t0) cc_final: 0.7694 (t0) REVERT: N 76 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9072 (ttmm) REVERT: N 106 ASP cc_start: 0.8691 (p0) cc_final: 0.8417 (p0) REVERT: N 107 CYS cc_start: 0.8825 (p) cc_final: 0.8536 (m) REVERT: S 7 SER cc_start: 0.9403 (t) cc_final: 0.9019 (p) REVERT: S 73 ASP cc_start: 0.7164 (t70) cc_final: 0.6945 (t70) REVERT: C 6 CYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7686 (t) outliers start: 13 outliers final: 7 residues processed: 145 average time/residue: 1.6026 time to fit residues: 246.6867 Evaluate side-chains 145 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain B residue 52 ARG 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 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 4 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.0040 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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 ** 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 = 0.3498 r_free = 0.3498 target = 0.096468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062841 restraints weight = 19089.687| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.04 r_work: 0.2719 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10331 Z= 0.222 Angle : 0.613 10.228 14024 Z= 0.318 Chirality : 0.042 0.184 1574 Planarity : 0.004 0.040 1771 Dihedral : 4.620 43.017 1599 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.58 % Allowed : 14.88 % 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 (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: 1.59 (0.24), residues: 1259 helix: 2.80 (0.26), residues: 399 sheet: 0.85 (0.27), residues: 334 loop : -0.15 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 292 TYR 0.013 0.001 TYR R 117 ARG 0.012 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7895.91 seconds wall clock time: 140 minutes 13.95 seconds (8413.95 seconds total)