Starting phenix.real_space_refine on Tue May 13 07:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blw_44678/05_2025/9blw_44678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blw_44678/05_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_44678/05_2025/9blw_44678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blw_44678/05_2025/9blw_44678.map" model { file = "/net/cci-nas-00/data/ceres_data/9blw_44678/05_2025/9blw_44678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blw_44678/05_2025/9blw_44678.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} 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: 5.85, per 1000 atoms: 0.59 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.76 Time building geometry restraints manager: 2.92 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (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 TRP 0.013 0.001 TRP B 339 HIS 0.006 0.001 HIS R 336 PHE 0.009 0.001 PHE N 68 TYR 0.009 0.001 TYR R 191 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 0.60341 ( 3) hydrogen bonds : bond 0.14476 ( 515) hydrogen bonds : angle 6.42397 ( 1497) SS BOND : bond 0.00160 ( 9) SS BOND : angle 1.10225 ( 18) covalent geometry : bond 0.00216 (10198) covalent geometry : angle 0.52435 (13845) Misc. bond : bond 0.10759 ( 1) *********************** 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 : 1.036 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 118 average time/residue: 0.2458 time to fit residues: 40.0701 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 : 1.082 ------------------------------------------------------------------------------- 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 103 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 186 ASN R 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.187113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.142692 restraints weight = 10119.988| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.80 r_work: 0.3347 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10209 Z= 0.231 Angle : 0.624 9.469 13866 Z= 0.333 Chirality : 0.046 0.239 1537 Planarity : 0.005 0.057 1768 Dihedral : 5.000 56.549 1404 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.62 % Allowed : 17.13 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1248 helix: 1.94 (0.23), residues: 505 sheet: 0.40 (0.33), residues: 244 loop : -0.23 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 47 HIS 0.006 0.002 HIS A 357 PHE 0.025 0.003 PHE N 68 TYR 0.014 0.002 TYR N 95 ARG 0.005 0.001 ARG A 385 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 0.82158 ( 3) hydrogen bonds : bond 0.04733 ( 515) hydrogen bonds : angle 4.62927 ( 1497) SS BOND : bond 0.00276 ( 9) SS BOND : angle 1.14663 ( 18) covalent geometry : bond 0.00545 (10198) covalent geometry : angle 0.62326 (13845) Misc. bond : bond 0.00071 ( 1) *********************** 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 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.006 Fit side-chains REVERT: A 239 ASN cc_start: 0.8551 (p0) cc_final: 0.8305 (p0) REVERT: B 10 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6823 (tp30) REVERT: N 63 SER cc_start: 0.9194 (t) cc_final: 0.8826 (p) REVERT: E 122 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (t80) REVERT: R 306 MET cc_start: 0.8804 (mmm) cc_final: 0.8555 (mmt) REVERT: R 405 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7319 (mp10) outliers start: 38 outliers final: 26 residues processed: 156 average time/residue: 0.2279 time to fit residues: 49.8476 Evaluate side-chains 149 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 349 SER 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 196 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 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 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 197 ILE 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 60 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 111 optimal weight: 0.6980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN P 31 ASN R 60 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.189807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144732 restraints weight = 10131.606| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.48 r_work: 0.3392 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2036 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= 0.128 Angle : 0.499 9.566 13866 Z= 0.267 Chirality : 0.041 0.230 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.586 55.398 1400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.38 % Allowed : 19.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1248 helix: 2.25 (0.23), residues: 507 sheet: 0.36 (0.33), residues: 244 loop : -0.25 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 0.83317 ( 3) hydrogen bonds : bond 0.03883 ( 515) hydrogen bonds : angle 4.23991 ( 1497) SS BOND : bond 0.00173 ( 9) SS BOND : angle 0.70929 ( 18) covalent geometry : bond 0.00290 (10198) covalent geometry : angle 0.49812 (13845) Misc. bond : bond 0.00082 ( 1) *********************** 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 151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.123 Fit side-chains REVERT: A 239 ASN cc_start: 0.8531 (p0) cc_final: 0.8310 (p0) REVERT: A 274 ASP cc_start: 0.7582 (t0) cc_final: 0.7139 (t0) REVERT: B 10 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: N 63 SER cc_start: 0.9155 (t) cc_final: 0.8812 (p) REVERT: N 87 LYS cc_start: 0.7037 (mttt) cc_final: 0.6075 (mptt) REVERT: E 122 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8146 (t80) REVERT: R 306 MET cc_start: 0.8643 (mmm) cc_final: 0.8403 (mmt) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 0.2365 time to fit residues: 47.7512 Evaluate side-chains 144 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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 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 264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4035 r_free = 0.4035 target = 0.189820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.145071 restraints weight = 10097.731| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.56 r_work: 0.3401 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2146 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= 0.117 Angle : 0.485 9.627 13866 Z= 0.258 Chirality : 0.040 0.229 1537 Planarity : 0.004 0.049 1768 Dihedral : 4.535 55.405 1400 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.81 % Allowed : 18.46 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1248 helix: 2.35 (0.23), residues: 507 sheet: 0.28 (0.32), residues: 244 loop : -0.23 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR N 60 ARG 0.005 0.000 ARG A 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 0.74672 ( 3) hydrogen bonds : bond 0.03634 ( 515) hydrogen bonds : angle 4.09102 ( 1497) SS BOND : bond 0.00164 ( 9) SS BOND : angle 1.39436 ( 18) covalent geometry : bond 0.00262 (10198) covalent geometry : angle 0.48217 (13845) Misc. bond : bond 0.00062 ( 1) *********************** 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 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 1.020 Fit side-chains REVERT: A 239 ASN cc_start: 0.8564 (p0) cc_final: 0.8331 (p0) REVERT: A 274 ASP cc_start: 0.7592 (t0) cc_final: 0.7112 (t0) REVERT: B 10 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6751 (tp30) REVERT: B 219 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6852 (mtm180) REVERT: N 87 LYS cc_start: 0.6943 (mttt) cc_final: 0.6017 (mptt) REVERT: E 122 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8111 (t80) REVERT: R 172 PHE cc_start: 0.7063 (t80) cc_final: 0.6430 (t80) REVERT: R 306 MET cc_start: 0.8610 (mmm) cc_final: 0.8359 (mmt) REVERT: R 405 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6213 (mp10) outliers start: 40 outliers final: 28 residues processed: 153 average time/residue: 0.2233 time to fit residues: 47.6211 Evaluate side-chains 149 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 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 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 247 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4028 r_free = 0.4028 target = 0.188630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145245 restraints weight = 10176.790| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.48 r_work: 0.3371 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10209 Z= 0.118 Angle : 0.478 9.633 13866 Z= 0.253 Chirality : 0.040 0.228 1537 Planarity : 0.004 0.049 1768 Dihedral : 4.491 55.324 1400 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.81 % Allowed : 18.84 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1248 helix: 2.38 (0.23), residues: 513 sheet: 0.18 (0.32), residues: 244 loop : -0.35 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 336 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 0.75702 ( 3) hydrogen bonds : bond 0.03557 ( 515) hydrogen bonds : angle 3.99296 ( 1497) SS BOND : bond 0.00275 ( 9) SS BOND : angle 1.06453 ( 18) covalent geometry : bond 0.00266 (10198) covalent geometry : angle 0.47691 (13845) Misc. bond : bond 0.00062 ( 1) *********************** 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: 40 poor density : 121 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8666 (p0) cc_final: 0.8459 (p0) REVERT: A 274 ASP cc_start: 0.7547 (t0) cc_final: 0.7055 (t0) REVERT: B 10 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: B 134 ARG cc_start: 0.5715 (ttp-110) cc_final: 0.5500 (ttp-110) REVERT: B 219 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6791 (mtm180) REVERT: E 93 PHE cc_start: 0.8426 (m-80) cc_final: 0.8059 (m-80) REVERT: E 122 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8095 (t80) REVERT: R 172 PHE cc_start: 0.7090 (t80) cc_final: 0.6419 (t80) REVERT: R 306 MET cc_start: 0.8597 (mmm) cc_final: 0.8336 (mmt) outliers start: 40 outliers final: 29 residues processed: 151 average time/residue: 0.2227 time to fit residues: 47.4944 Evaluate side-chains 152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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 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 405 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4001 r_free = 0.4001 target = 0.185928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.141758 restraints weight = 10218.587| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.99 r_work: 0.3310 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2559 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= 0.148 Angle : 0.528 9.661 13866 Z= 0.278 Chirality : 0.042 0.227 1537 Planarity : 0.004 0.049 1768 Dihedral : 4.687 55.369 1400 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.28 % Allowed : 19.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1248 helix: 2.28 (0.23), residues: 513 sheet: 0.05 (0.32), residues: 250 loop : -0.42 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 199 TYR 0.012 0.001 TYR R 149 ARG 0.005 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 0.90895 ( 3) hydrogen bonds : bond 0.03865 ( 515) hydrogen bonds : angle 4.07786 ( 1497) SS BOND : bond 0.00422 ( 9) SS BOND : angle 2.60619 ( 18) covalent geometry : bond 0.00345 (10198) covalent geometry : angle 0.51946 (13845) Misc. bond : bond 0.00054 ( 1) *********************** 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 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 1.132 Fit side-chains REVERT: A 239 ASN cc_start: 0.8744 (p0) cc_final: 0.8515 (p0) REVERT: B 10 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: B 59 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 134 ARG cc_start: 0.5720 (ttp-110) cc_final: 0.5481 (ttp-110) REVERT: B 219 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6803 (mtm180) REVERT: E 93 PHE cc_start: 0.8561 (m-80) cc_final: 0.8158 (m-80) REVERT: E 122 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8141 (t80) REVERT: R 172 PHE cc_start: 0.7175 (t80) cc_final: 0.6466 (t80) REVERT: R 221 ILE cc_start: 0.7367 (mt) cc_final: 0.7092 (mp) REVERT: R 306 MET cc_start: 0.8693 (mmm) cc_final: 0.8433 (mmt) REVERT: R 316 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7973 (tp) REVERT: R 405 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6123 (mp10) outliers start: 45 outliers final: 36 residues processed: 164 average time/residue: 0.2285 time to fit residues: 52.3416 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 P residue 7 CYS 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 316 LEU Chi-restraints excluded: chain R residue 320 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 105 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 110 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4028 r_free = 0.4028 target = 0.188512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143629 restraints weight = 10248.054| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.53 r_work: 0.3372 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2587 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= 0.112 Angle : 0.486 9.631 13866 Z= 0.255 Chirality : 0.040 0.230 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.539 55.481 1400 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.90 % Allowed : 19.89 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1248 helix: 2.40 (0.23), residues: 513 sheet: 0.13 (0.32), residues: 244 loop : -0.44 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 0.72385 ( 3) hydrogen bonds : bond 0.03499 ( 515) hydrogen bonds : angle 3.94430 ( 1497) SS BOND : bond 0.00205 ( 9) SS BOND : angle 1.87969 ( 18) covalent geometry : bond 0.00250 (10198) covalent geometry : angle 0.48124 (13845) Misc. bond : bond 0.00054 ( 1) *********************** 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 171 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7548 (t0) cc_final: 0.7240 (t0) REVERT: B 10 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6876 (tp30) REVERT: B 59 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 134 ARG cc_start: 0.5716 (ttp-110) cc_final: 0.5464 (ttp-110) REVERT: B 219 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6807 (mtm180) REVERT: G 42 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6364 (mt-10) REVERT: E 93 PHE cc_start: 0.8515 (m-80) cc_final: 0.8189 (m-80) REVERT: E 122 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (t80) REVERT: R 172 PHE cc_start: 0.7084 (t80) cc_final: 0.6398 (t80) REVERT: R 221 ILE cc_start: 0.7424 (mt) cc_final: 0.7186 (mp) REVERT: R 306 MET cc_start: 0.8562 (mmm) cc_final: 0.8308 (mmt) outliers start: 41 outliers final: 30 residues processed: 162 average time/residue: 0.2196 time to fit residues: 50.0256 Evaluate side-chains 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 59 TYR 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 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 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 42 GLU 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 247 LEU Chi-restraints excluded: chain R residue 264 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4018 r_free = 0.4018 target = 0.187502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146899 restraints weight = 10279.753| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.44 r_work: 0.3363 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10209 Z= 0.123 Angle : 0.501 9.638 13866 Z= 0.262 Chirality : 0.041 0.251 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.558 55.496 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 : 3.81 % Allowed : 19.89 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1248 helix: 2.44 (0.23), residues: 507 sheet: 0.03 (0.32), residues: 250 loop : -0.34 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 332 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 0.78720 ( 3) hydrogen bonds : bond 0.03587 ( 515) hydrogen bonds : angle 3.99330 ( 1497) SS BOND : bond 0.00229 ( 9) SS BOND : angle 1.55549 ( 18) covalent geometry : bond 0.00282 (10198) covalent geometry : angle 0.49842 (13845) Misc. bond : bond 0.00053 ( 1) *********************** 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 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.091 Fit side-chains REVERT: A 274 ASP cc_start: 0.7592 (t0) cc_final: 0.7374 (t0) REVERT: B 10 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: B 59 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7741 (t80) REVERT: B 134 ARG cc_start: 0.5717 (ttp-110) cc_final: 0.5454 (ttp-110) REVERT: B 219 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6853 (mtm180) REVERT: G 42 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6446 (mt-10) REVERT: E 83 PHE cc_start: 0.4470 (OUTLIER) cc_final: 0.4238 (t80) REVERT: E 93 PHE cc_start: 0.8515 (m-80) cc_final: 0.8170 (m-80) REVERT: E 122 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8112 (t80) REVERT: R 172 PHE cc_start: 0.7109 (t80) cc_final: 0.6444 (t80) REVERT: R 221 ILE cc_start: 0.7430 (mt) cc_final: 0.7191 (mp) REVERT: R 306 MET cc_start: 0.8587 (mmm) cc_final: 0.8325 (mmt) REVERT: R 405 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6178 (mp10) outliers start: 40 outliers final: 32 residues processed: 155 average time/residue: 0.2256 time to fit residues: 49.0921 Evaluate side-chains 159 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 37 LEU Chi-restraints excluded: chain G residue 42 GLU 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 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 101 ASP 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 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 96 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 40.0000 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.184586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142908 restraints weight = 10277.934| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.48 r_work: 0.3321 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10209 Z= 0.164 Angle : 0.537 9.663 13866 Z= 0.282 Chirality : 0.043 0.228 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.718 55.444 1400 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.90 % Allowed : 19.89 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1248 helix: 2.28 (0.23), residues: 507 sheet: -0.09 (0.31), residues: 250 loop : -0.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE B 241 TYR 0.012 0.001 TYR R 149 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 0.92544 ( 3) hydrogen bonds : bond 0.03946 ( 515) hydrogen bonds : angle 4.15727 ( 1497) SS BOND : bond 0.00263 ( 9) SS BOND : angle 1.46299 ( 18) covalent geometry : bond 0.00386 (10198) covalent geometry : angle 0.53484 (13845) Misc. bond : bond 0.00047 ( 1) *********************** 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 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: B 59 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 134 ARG cc_start: 0.5712 (ttp-110) cc_final: 0.5445 (ttp-110) REVERT: B 219 ARG cc_start: 0.7170 (mtm110) cc_final: 0.6823 (mtm180) REVERT: G 42 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: E 83 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.4286 (t80) REVERT: E 93 PHE cc_start: 0.8582 (m-80) cc_final: 0.8220 (m-80) REVERT: E 122 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8132 (t80) REVERT: R 172 PHE cc_start: 0.7107 (t80) cc_final: 0.6424 (t80) REVERT: R 306 MET cc_start: 0.8665 (mmm) cc_final: 0.8402 (mmt) REVERT: R 405 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6376 (mp10) outliers start: 41 outliers final: 33 residues processed: 158 average time/residue: 0.2350 time to fit residues: 52.2272 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 37 LEU Chi-restraints excluded: chain G residue 42 GLU 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 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 P residue 7 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.183441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140037 restraints weight = 10282.457| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.55 r_work: 0.3299 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10209 Z= 0.180 Angle : 0.558 9.676 13866 Z= 0.293 Chirality : 0.043 0.227 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.838 55.385 1400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.81 % Allowed : 20.27 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1248 helix: 2.12 (0.23), residues: 507 sheet: -0.21 (0.31), residues: 250 loop : -0.48 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE N 68 TYR 0.014 0.002 TYR R 149 ARG 0.005 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 0.99832 ( 3) hydrogen bonds : bond 0.04139 ( 515) hydrogen bonds : angle 4.29571 ( 1497) SS BOND : bond 0.00292 ( 9) SS BOND : angle 1.45019 ( 18) covalent geometry : bond 0.00426 (10198) covalent geometry : angle 0.55577 (13845) Misc. bond : bond 0.00040 ( 1) ********************** 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 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: B 59 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7739 (t80) REVERT: B 134 ARG cc_start: 0.5788 (ttp-110) cc_final: 0.5527 (ttp-110) REVERT: B 219 ARG cc_start: 0.7178 (mtm110) cc_final: 0.6864 (mtm180) REVERT: G 42 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: N 63 SER cc_start: 0.9077 (t) cc_final: 0.8729 (p) REVERT: E 83 PHE cc_start: 0.4663 (OUTLIER) cc_final: 0.4420 (t80) REVERT: E 93 PHE cc_start: 0.8562 (m-80) cc_final: 0.8201 (m-80) REVERT: E 122 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (t80) REVERT: R 172 PHE cc_start: 0.7240 (t80) cc_final: 0.6576 (t80) REVERT: R 306 MET cc_start: 0.8684 (mmm) cc_final: 0.8429 (mmt) REVERT: R 405 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6530 (mp10) outliers start: 40 outliers final: 32 residues processed: 163 average time/residue: 0.2221 time to fit residues: 50.5786 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 226 GLU 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 37 LEU Chi-restraints excluded: chain G residue 42 GLU 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 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 P residue 7 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 0.0170 chunk 73 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4014 r_free = 0.4014 target = 0.187112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.142045 restraints weight = 10210.264| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.64 r_work: 0.3372 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10209 Z= 0.114 Angle : 0.494 9.634 13866 Z= 0.261 Chirality : 0.041 0.232 1537 Planarity : 0.004 0.052 1768 Dihedral : 4.594 55.602 1400 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.52 % Allowed : 20.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1248 helix: 2.23 (0.23), residues: 514 sheet: -0.18 (0.31), residues: 259 loop : -0.42 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR N 60 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 0.75079 ( 3) hydrogen bonds : bond 0.03554 ( 515) hydrogen bonds : angle 4.03940 ( 1497) SS BOND : bond 0.00228 ( 9) SS BOND : angle 1.12539 ( 18) covalent geometry : bond 0.00253 (10198) covalent geometry : angle 0.49273 (13845) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5614.35 seconds wall clock time: 97 minutes 45.14 seconds (5865.14 seconds total)