Starting phenix.real_space_refine on Wed Sep 17 16:49:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.map" model { file = "/net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blw_44678/09_2025/9blw_44678.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.091 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 72 5.16 5 C 6344 2.51 5 N 1732 2.21 5 O 1813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9961 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1857 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 777 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "P" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 276 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "P" 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: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3033 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.26 Number of scatterers: 9961 At special positions: 0 Unit cell: (77.4, 98.9, 164.26, 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 72 16.00 O 1813 8.00 N 1732 7.00 C 6344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 374.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 44.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.644A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.635A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.626A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.905A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.464A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.537A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 37 " --> pdb=" O THR B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 37' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.563A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.666A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 52 removed outlier: 3.717A pdb=" N LEU E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.532A pdb=" N CYS E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.652A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 144 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 17 removed outlier: 3.567A pdb=" N LEU P 12 " --> pdb=" O ALA P 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 62 Processing helix chain 'R' and resid 131 through 137 removed outlier: 3.682A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.532A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.818A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.728A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.638A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 4.061A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 391 removed outlier: 4.774A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR R 391 " --> pdb=" O VAL R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.478A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.815A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.768A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.074A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.582A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.702A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.696A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.712A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.596A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.811A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB5, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.716A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3236 1.35 - 1.46: 2528 1.46 - 1.58: 4333 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 10198 Sorted by residual: bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.06e+00 bond pdb=" N GLY P 33 " pdb=" CA GLY P 33 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.13e-02 7.83e+03 6.91e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.451 1.491 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N THR P 30 " pdb=" CA THR P 30 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.31e-02 5.83e+03 6.22e+00 bond pdb=" N ASN P 31 " pdb=" CA ASN P 31 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.41e+00 ... (remaining 10193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13801 3.05 - 6.10: 41 6.10 - 9.14: 1 9.14 - 12.19: 0 12.19 - 15.24: 2 Bond angle restraints: 13845 Sorted by residual: angle pdb=" CA PRO P 37 " pdb=" N PRO P 37 " pdb=" CD PRO P 37 " ideal model delta sigma weight residual 112.00 97.71 14.29 1.40e+00 5.10e-01 1.04e+02 angle pdb=" C THR P 36 " pdb=" N PRO P 37 " pdb=" CD PRO P 37 " ideal model delta sigma weight residual 125.00 140.24 -15.24 4.10e+00 5.95e-02 1.38e+01 angle pdb=" N SER P 34 " pdb=" CA SER P 34 " pdb=" C SER P 34 " ideal model delta sigma weight residual 111.28 107.24 4.04 1.09e+00 8.42e-01 1.37e+01 angle pdb=" O THR P 36 " pdb=" C THR P 36 " pdb=" N PRO P 37 " ideal model delta sigma weight residual 121.60 125.22 -3.62 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA ASN P 31 " pdb=" C ASN P 31 " pdb=" O ASN P 31 " ideal model delta sigma weight residual 120.82 117.31 3.51 1.05e+00 9.07e-01 1.12e+01 ... (remaining 13840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5262 17.46 - 34.92: 577 34.92 - 52.38: 160 52.38 - 69.84: 37 69.84 - 87.29: 13 Dihedral angle restraints: 6049 sinusoidal: 2359 harmonic: 3690 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -20.47 -65.53 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -147.22 61.22 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 152.85 -59.85 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 6046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1381 0.064 - 0.128: 152 0.128 - 0.192: 3 0.192 - 0.256: 0 0.256 - 0.319: 1 Chirality restraints: 1537 Sorted by residual: chirality pdb=" CA PRO P 37 " pdb=" N PRO P 37 " pdb=" C PRO P 37 " pdb=" CB PRO P 37 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2 NAG R 501 " pdb=" C1 NAG R 501 " pdb=" C3 NAG R 501 " pdb=" N2 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1534 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 138 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO R 139 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 139 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 139 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 35 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ASN P 35 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN P 35 " -0.014 2.00e-02 2.50e+03 pdb=" N THR P 36 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 323 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C LEU R 323 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU R 323 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL R 324 " 0.011 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2243 2.79 - 3.31: 9494 3.31 - 3.84: 16935 3.84 - 4.37: 19346 4.37 - 4.90: 33950 Nonbonded interactions: 81968 Sorted by model distance: nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.257 3.120 nonbonded pdb=" O ASN P 35 " pdb=" NH1 ARG R 126 " model vdw 2.280 3.120 nonbonded pdb=" OE1 GLN N 39 " pdb=" OH TYR N 95 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.283 3.040 nonbonded pdb=" O GLU R 397 " pdb=" OG1 THR R 401 " model vdw 2.288 3.040 ... (remaining 81963 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=0.00 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.002 0.108 10209 Z= 0.167 Angle : 0.526 15.240 13866 Z= 0.307 Chirality : 0.040 0.319 1537 Planarity : 0.004 0.062 1768 Dihedral : 16.254 87.295 3638 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.38 % Allowed : 19.60 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.24), residues: 1248 helix: 1.60 (0.24), residues: 494 sheet: 0.85 (0.34), residues: 229 loop : -0.22 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.009 0.001 TYR R 191 PHE 0.009 0.001 PHE N 68 TRP 0.013 0.001 TRP B 339 HIS 0.006 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00216 (10198) covalent geometry : angle 0.52435 (13845) SS BOND : bond 0.00160 ( 9) SS BOND : angle 1.10225 ( 18) hydrogen bonds : bond 0.14476 ( 515) hydrogen bonds : angle 6.42397 ( 1497) Misc. bond : bond 0.10759 ( 1) link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 0.60341 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 118 average time/residue: 0.1198 time to fit residues: 19.4587 Evaluate side-chains 115 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain R residue 199 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN N 39 GLN N 82 GLN R 60 GLN R 186 ASN R 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.188386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144572 restraints weight = 10120.833| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.49 r_work: 0.3375 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10209 Z= 0.214 Angle : 0.602 9.346 13866 Z= 0.322 Chirality : 0.045 0.216 1537 Planarity : 0.004 0.058 1768 Dihedral : 4.880 55.929 1404 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.85 % Allowed : 17.98 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1248 helix: 1.91 (0.23), residues: 512 sheet: 0.39 (0.33), residues: 246 loop : -0.23 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 336 TYR 0.014 0.002 TYR N 95 PHE 0.023 0.002 PHE N 68 TRP 0.016 0.002 TRP N 47 HIS 0.006 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00500 (10198) covalent geometry : angle 0.60151 (13845) SS BOND : bond 0.00260 ( 9) SS BOND : angle 1.09028 ( 18) hydrogen bonds : bond 0.04625 ( 515) hydrogen bonds : angle 4.61248 ( 1497) Misc. bond : bond 0.00076 ( 1) link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 0.49106 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.373 Fit side-chains REVERT: A 239 ASN cc_start: 0.8433 (p0) cc_final: 0.8191 (p0) REVERT: B 10 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: N 63 SER cc_start: 0.9178 (t) cc_final: 0.8792 (p) REVERT: N 68 PHE cc_start: 0.7432 (m-10) cc_final: 0.7232 (m-10) REVERT: N 99 CYS cc_start: 0.6571 (t) cc_final: 0.6316 (t) REVERT: E 122 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8147 (t80) REVERT: R 306 MET cc_start: 0.8741 (mmm) cc_final: 0.8487 (mmt) REVERT: R 405 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7308 (mp10) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.1118 time to fit residues: 23.1559 Evaluate side-chains 143 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN G 59 ASN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.192238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.151132 restraints weight = 10089.795| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.40 r_work: 0.3413 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10209 Z= 0.108 Angle : 0.474 9.530 13866 Z= 0.254 Chirality : 0.040 0.232 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.446 55.448 1400 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.38 % Allowed : 19.22 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.24), residues: 1248 helix: 2.36 (0.23), residues: 507 sheet: 0.36 (0.33), residues: 246 loop : -0.18 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.013 0.001 TYR N 60 PHE 0.015 0.001 PHE N 27 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00236 (10198) covalent geometry : angle 0.47384 (13845) SS BOND : bond 0.00131 ( 9) SS BOND : angle 0.61221 ( 18) hydrogen bonds : bond 0.03650 ( 515) hydrogen bonds : angle 4.13862 ( 1497) Misc. bond : bond 0.00084 ( 1) link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 0.74376 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.265 Fit side-chains REVERT: A 239 ASN cc_start: 0.8435 (p0) cc_final: 0.8222 (p0) REVERT: A 274 ASP cc_start: 0.7577 (t0) cc_final: 0.7093 (t0) REVERT: B 10 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: N 34 MET cc_start: 0.8245 (mmm) cc_final: 0.7995 (mmm) REVERT: N 63 SER cc_start: 0.9163 (t) cc_final: 0.8810 (p) REVERT: N 87 LYS cc_start: 0.7007 (mttt) cc_final: 0.6089 (mptt) REVERT: E 122 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8089 (t80) REVERT: R 306 MET cc_start: 0.8619 (mmm) cc_final: 0.8377 (mmt) outliers start: 25 outliers final: 15 residues processed: 144 average time/residue: 0.1166 time to fit residues: 23.0525 Evaluate side-chains 138 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.189894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147437 restraints weight = 10254.937| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.47 r_work: 0.3377 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10209 Z= 0.130 Angle : 0.492 9.638 13866 Z= 0.261 Chirality : 0.041 0.228 1537 Planarity : 0.004 0.047 1768 Dihedral : 4.530 55.379 1400 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.52 % Allowed : 18.27 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1248 helix: 2.35 (0.23), residues: 507 sheet: 0.20 (0.32), residues: 242 loop : -0.19 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.011 0.001 TYR N 60 PHE 0.014 0.001 PHE N 108 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00296 (10198) covalent geometry : angle 0.48967 (13845) SS BOND : bond 0.00499 ( 9) SS BOND : angle 1.25306 ( 18) hydrogen bonds : bond 0.03722 ( 515) hydrogen bonds : angle 4.11977 ( 1497) Misc. bond : bond 0.00064 ( 1) link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 0.79765 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.448 Fit side-chains REVERT: A 274 ASP cc_start: 0.7675 (t0) cc_final: 0.7209 (t0) REVERT: B 10 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: N 87 LYS cc_start: 0.6978 (mttt) cc_final: 0.6022 (mptt) REVERT: E 122 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8132 (t80) REVERT: R 172 PHE cc_start: 0.7057 (t80) cc_final: 0.6451 (t80) REVERT: R 306 MET cc_start: 0.8667 (mmm) cc_final: 0.8423 (mmt) REVERT: R 405 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6198 (mp10) outliers start: 37 outliers final: 27 residues processed: 158 average time/residue: 0.1078 time to fit residues: 24.0303 Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.190950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.145182 restraints weight = 10197.350| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.56 r_work: 0.3416 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10209 Z= 0.108 Angle : 0.473 9.627 13866 Z= 0.250 Chirality : 0.040 0.229 1537 Planarity : 0.004 0.048 1768 Dihedral : 4.486 55.318 1400 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.71 % Allowed : 18.65 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1248 helix: 2.50 (0.23), residues: 507 sheet: 0.24 (0.32), residues: 243 loop : -0.22 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 105 TYR 0.012 0.001 TYR N 60 PHE 0.011 0.001 PHE A 212 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00241 (10198) covalent geometry : angle 0.47010 (13845) SS BOND : bond 0.00186 ( 9) SS BOND : angle 1.40752 ( 18) hydrogen bonds : bond 0.03455 ( 515) hydrogen bonds : angle 3.94592 ( 1497) Misc. bond : bond 0.00058 ( 1) link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 0.73032 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8432 (p0) cc_final: 0.8211 (p0) REVERT: A 274 ASP cc_start: 0.7548 (t0) cc_final: 0.7056 (t0) REVERT: B 10 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6736 (tp30) REVERT: B 219 ARG cc_start: 0.7122 (mtm110) cc_final: 0.6697 (mtm180) REVERT: E 93 PHE cc_start: 0.8409 (m-80) cc_final: 0.8042 (m-80) REVERT: E 122 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8066 (t80) REVERT: R 172 PHE cc_start: 0.7053 (t80) cc_final: 0.6440 (t80) REVERT: R 306 MET cc_start: 0.8567 (mmm) cc_final: 0.8317 (mmt) outliers start: 39 outliers final: 29 residues processed: 149 average time/residue: 0.1126 time to fit residues: 23.4461 Evaluate side-chains 151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.191219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146786 restraints weight = 10240.659| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.09 r_work: 0.3365 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10209 Z= 0.106 Angle : 0.475 9.618 13866 Z= 0.250 Chirality : 0.040 0.229 1537 Planarity : 0.004 0.048 1768 Dihedral : 4.463 55.340 1400 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.00 % Allowed : 18.74 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1248 helix: 2.56 (0.23), residues: 506 sheet: 0.23 (0.32), residues: 243 loop : -0.24 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.012 0.001 TYR N 60 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP B 332 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00235 (10198) covalent geometry : angle 0.47032 (13845) SS BOND : bond 0.00231 ( 9) SS BOND : angle 1.92793 ( 18) hydrogen bonds : bond 0.03392 ( 515) hydrogen bonds : angle 3.87446 ( 1497) Misc. bond : bond 0.00052 ( 1) link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 0.73872 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8448 (p0) cc_final: 0.8188 (p0) REVERT: A 274 ASP cc_start: 0.7566 (t0) cc_final: 0.6922 (t70) REVERT: B 10 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: B 59 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 219 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6773 (mtm180) REVERT: E 93 PHE cc_start: 0.8489 (m-80) cc_final: 0.8101 (m-80) REVERT: E 122 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7959 (t80) REVERT: R 172 PHE cc_start: 0.7107 (t80) cc_final: 0.6445 (t80) REVERT: R 306 MET cc_start: 0.8588 (mmm) cc_final: 0.8312 (mmt) outliers start: 42 outliers final: 33 residues processed: 154 average time/residue: 0.1057 time to fit residues: 23.0494 Evaluate side-chains 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.187463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145084 restraints weight = 10192.146| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.51 r_work: 0.3348 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10209 Z= 0.135 Angle : 0.508 9.641 13866 Z= 0.266 Chirality : 0.042 0.233 1537 Planarity : 0.004 0.047 1768 Dihedral : 4.564 55.298 1400 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.28 % Allowed : 18.84 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.24), residues: 1248 helix: 2.45 (0.23), residues: 507 sheet: 0.08 (0.32), residues: 244 loop : -0.32 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.011 0.001 TYR N 60 PHE 0.014 0.001 PHE B 241 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00316 (10198) covalent geometry : angle 0.50517 (13845) SS BOND : bond 0.00269 ( 9) SS BOND : angle 1.63826 ( 18) hydrogen bonds : bond 0.03686 ( 515) hydrogen bonds : angle 3.99356 ( 1497) Misc. bond : bond 0.00058 ( 1) link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 0.84767 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8556 (p0) cc_final: 0.8310 (p0) REVERT: A 274 ASP cc_start: 0.7628 (t0) cc_final: 0.7282 (t0) REVERT: B 10 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: B 59 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 138 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 219 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6768 (mtm180) REVERT: E 93 PHE cc_start: 0.8512 (m-80) cc_final: 0.8178 (m-80) REVERT: E 122 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8074 (t80) REVERT: R 172 PHE cc_start: 0.7101 (t80) cc_final: 0.6428 (t80) REVERT: R 221 ILE cc_start: 0.7337 (mt) cc_final: 0.7096 (mp) REVERT: R 306 MET cc_start: 0.8639 (mmm) cc_final: 0.8387 (mmt) outliers start: 45 outliers final: 36 residues processed: 165 average time/residue: 0.1077 time to fit residues: 24.9885 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 39 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 336 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.190958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143860 restraints weight = 10129.486| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.46 r_work: 0.3424 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10209 Z= 0.097 Angle : 0.470 9.615 13866 Z= 0.246 Chirality : 0.040 0.231 1537 Planarity : 0.004 0.048 1768 Dihedral : 4.414 55.611 1400 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.95 % Allowed : 20.36 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.24), residues: 1248 helix: 2.55 (0.23), residues: 506 sheet: 0.34 (0.33), residues: 230 loop : -0.32 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR N 60 PHE 0.011 0.001 PHE A 212 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00208 (10198) covalent geometry : angle 0.46808 (13845) SS BOND : bond 0.00194 ( 9) SS BOND : angle 1.16954 ( 18) hydrogen bonds : bond 0.03255 ( 515) hydrogen bonds : angle 3.84374 ( 1497) Misc. bond : bond 0.00054 ( 1) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 0.66852 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.361 Fit side-chains REVERT: A 239 ASN cc_start: 0.8455 (p0) cc_final: 0.8192 (p0) REVERT: B 10 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: B 59 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7763 (t80) REVERT: B 219 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6770 (mtm180) REVERT: E 93 PHE cc_start: 0.8507 (m-80) cc_final: 0.8154 (m-80) REVERT: E 122 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7975 (t80) REVERT: R 172 PHE cc_start: 0.7047 (t80) cc_final: 0.6393 (t80) REVERT: R 306 MET cc_start: 0.8492 (mmm) cc_final: 0.8203 (mmt) REVERT: R 405 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6002 (mp10) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.1083 time to fit residues: 22.7436 Evaluate side-chains 151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 56 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.191065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144069 restraints weight = 10169.039| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.45 r_work: 0.3429 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10209 Z= 0.096 Angle : 0.464 9.601 13866 Z= 0.242 Chirality : 0.040 0.231 1537 Planarity : 0.004 0.048 1768 Dihedral : 4.295 55.428 1400 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 19.98 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.24), residues: 1248 helix: 2.60 (0.23), residues: 506 sheet: 0.27 (0.33), residues: 241 loop : -0.26 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR N 60 PHE 0.010 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00209 (10198) covalent geometry : angle 0.46288 (13845) SS BOND : bond 0.00226 ( 9) SS BOND : angle 1.06499 ( 18) hydrogen bonds : bond 0.03192 ( 515) hydrogen bonds : angle 3.78535 ( 1497) Misc. bond : bond 0.00058 ( 1) link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 0.67093 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.395 Fit side-chains REVERT: A 239 ASN cc_start: 0.8456 (p0) cc_final: 0.8177 (p0) REVERT: A 274 ASP cc_start: 0.7427 (t0) cc_final: 0.6781 (t70) REVERT: B 10 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: B 59 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7770 (t80) REVERT: B 219 ARG cc_start: 0.7111 (mtm110) cc_final: 0.6735 (mtm180) REVERT: N 57 SER cc_start: 0.7599 (t) cc_final: 0.7334 (m) REVERT: E 83 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.4206 (t80) REVERT: E 93 PHE cc_start: 0.8487 (m-80) cc_final: 0.8125 (m-80) REVERT: E 122 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7868 (t80) REVERT: R 172 PHE cc_start: 0.7030 (t80) cc_final: 0.6347 (t80) REVERT: R 221 ILE cc_start: 0.7165 (mt) cc_final: 0.6923 (mp) REVERT: R 306 MET cc_start: 0.8494 (mmm) cc_final: 0.8185 (mmt) REVERT: R 405 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.5939 (mp10) outliers start: 35 outliers final: 28 residues processed: 147 average time/residue: 0.1117 time to fit residues: 23.0094 Evaluate side-chains 154 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 0.0000 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.188937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141544 restraints weight = 10075.413| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.45 r_work: 0.3396 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10209 Z= 0.118 Angle : 0.489 9.617 13866 Z= 0.256 Chirality : 0.041 0.230 1537 Planarity : 0.004 0.047 1768 Dihedral : 4.319 55.399 1400 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.43 % Allowed : 20.08 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.24), residues: 1248 helix: 2.50 (0.23), residues: 507 sheet: 0.16 (0.32), residues: 243 loop : -0.31 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.014 0.001 TYR N 60 PHE 0.018 0.001 PHE N 68 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00268 (10198) covalent geometry : angle 0.48791 (13845) SS BOND : bond 0.00262 ( 9) SS BOND : angle 1.09794 ( 18) hydrogen bonds : bond 0.03465 ( 515) hydrogen bonds : angle 3.88642 ( 1497) Misc. bond : bond 0.00051 ( 1) link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 0.75870 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.377 Fit side-chains REVERT: A 239 ASN cc_start: 0.8538 (p0) cc_final: 0.8278 (p0) REVERT: A 274 ASP cc_start: 0.7494 (t0) cc_final: 0.7016 (t0) REVERT: B 10 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6835 (tp30) REVERT: B 59 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 219 ARG cc_start: 0.7099 (mtm110) cc_final: 0.6748 (mtm180) REVERT: E 83 PHE cc_start: 0.4475 (OUTLIER) cc_final: 0.4226 (t80) REVERT: E 93 PHE cc_start: 0.8485 (m-80) cc_final: 0.8120 (m-80) REVERT: E 122 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7938 (t80) REVERT: R 172 PHE cc_start: 0.7000 (t80) cc_final: 0.6312 (t80) REVERT: R 221 ILE cc_start: 0.7226 (mt) cc_final: 0.7012 (mp) REVERT: R 306 MET cc_start: 0.8562 (mmm) cc_final: 0.8277 (mmt) REVERT: R 405 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6119 (mp10) outliers start: 36 outliers final: 30 residues processed: 148 average time/residue: 0.1108 time to fit residues: 23.0545 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** R 121 HIS ** 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 = 0.4044 r_free = 0.4044 target = 0.190082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144604 restraints weight = 10254.373| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.62 r_work: 0.3404 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10209 Z= 0.106 Angle : 0.487 9.610 13866 Z= 0.254 Chirality : 0.040 0.231 1537 Planarity : 0.004 0.048 1768 Dihedral : 4.313 55.476 1400 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.43 % Allowed : 20.46 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1248 helix: 2.56 (0.23), residues: 506 sheet: 0.20 (0.32), residues: 243 loop : -0.28 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR N 60 PHE 0.017 0.001 PHE N 68 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00235 (10198) covalent geometry : angle 0.47867 (13845) SS BOND : bond 0.00370 ( 9) SS BOND : angle 2.51756 ( 18) hydrogen bonds : bond 0.03327 ( 515) hydrogen bonds : angle 3.81877 ( 1497) Misc. bond : bond 0.00048 ( 1) link_NAG-ASN : bond 0.00128 ( 1) link_NAG-ASN : angle 0.70356 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.59 seconds wall clock time: 52 minutes 17.49 seconds (3137.49 seconds total)