Starting phenix.real_space_refine on Sun Jun 8 18:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blw_44678/06_2025/9blw_44678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blw_44678/06_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_44678/06_2025/9blw_44678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blw_44678/06_2025/9blw_44678.map" model { file = "/net/cci-nas-00/data/ceres_data/9blw_44678/06_2025/9blw_44678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blw_44678/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.94, per 1000 atoms: 0.60 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: 2.41 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: 1.00 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: 3.00 Time building geometry restraints manager: 2.89 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: 1.460 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.750 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- 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 : 1.056 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 118 average time/residue: 0.2712 time to fit residues: 44.1399 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 : 1.399 ------------------------------------------------------------------------------- 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 = 0.142691 restraints weight = 10119.993| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.80 r_work: 0.3348 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 0.82156 ( 3) hydrogen bonds : bond 0.04733 ( 515) hydrogen bonds : angle 4.62928 ( 1497) SS BOND : bond 0.00276 ( 9) SS BOND : angle 1.14664 ( 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 : 1.226 Fit side-chains REVERT: A 239 ASN cc_start: 0.8548 (p0) cc_final: 0.8304 (p0) REVERT: B 10 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: N 63 SER cc_start: 0.9199 (t) cc_final: 0.8833 (p) REVERT: E 122 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8241 (t80) REVERT: R 306 MET cc_start: 0.8804 (mmm) cc_final: 0.8559 (mmt) REVERT: R 405 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7330 (mp10) outliers start: 38 outliers final: 26 residues processed: 156 average time/residue: 0.2410 time to fit residues: 52.8538 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 : 1.023 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.189203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.147054 restraints weight = 10135.937| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.45 r_work: 0.3372 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2061 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= 0.135 Angle : 0.507 9.603 13866 Z= 0.271 Chirality : 0.041 0.230 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.625 55.404 1400 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.66 % Allowed : 19.12 % 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: 1.29 (0.24), residues: 1248 helix: 2.22 (0.23), residues: 507 sheet: 0.35 (0.33), residues: 244 loop : -0.26 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 0.86549 ( 3) hydrogen bonds : bond 0.03956 ( 515) hydrogen bonds : angle 4.28064 ( 1497) SS BOND : bond 0.00172 ( 9) SS BOND : angle 0.72322 ( 18) covalent geometry : bond 0.00307 (10198) covalent geometry : angle 0.50685 (13845) Misc. bond : bond 0.00076 ( 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 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.089 Fit side-chains REVERT: A 239 ASN cc_start: 0.8552 (p0) cc_final: 0.8332 (p0) REVERT: B 10 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: N 63 SER cc_start: 0.9166 (t) cc_final: 0.8820 (p) REVERT: N 87 LYS cc_start: 0.7014 (mttt) cc_final: 0.6045 (mptt) REVERT: E 122 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8146 (t80) REVERT: R 306 MET cc_start: 0.8681 (mmm) cc_final: 0.8437 (mmt) outliers start: 28 outliers final: 19 residues processed: 148 average time/residue: 0.2743 time to fit residues: 56.8381 Evaluate side-chains 143 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 228 ASP 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 Chi-restraints excluded: chain R residue 335 SER 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: 0.6980 chunk 17 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.189848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144395 restraints weight = 10103.250| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.71 r_work: 0.3389 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- 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 0.053 10209 Z= 0.116 Angle : 0.481 9.632 13866 Z= 0.256 Chirality : 0.040 0.229 1537 Planarity : 0.004 0.050 1768 Dihedral : 4.510 55.399 1400 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.71 % Allowed : 18.74 % Favored : 77.55 % 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: 0.30 (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 A 234 HIS 0.004 0.001 HIS R 336 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG A 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 1) link_NAG-ASN : angle 0.75203 ( 3) hydrogen bonds : bond 0.03637 ( 515) hydrogen bonds : angle 4.11902 ( 1497) SS BOND : bond 0.00227 ( 9) SS BOND : angle 1.04932 ( 18) covalent geometry : bond 0.00262 (10198) covalent geometry : angle 0.47929 (13845) Misc. bond : bond 0.00059 ( 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 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.329 Fit side-chains REVERT: A 239 ASN cc_start: 0.8577 (p0) cc_final: 0.8341 (p0) REVERT: A 274 ASP cc_start: 0.7544 (t0) cc_final: 0.7076 (t0) REVERT: B 10 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6753 (tp30) REVERT: B 219 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6834 (mtm180) REVERT: N 87 LYS cc_start: 0.6898 (mttt) cc_final: 0.5961 (mptt) REVERT: N 99 CYS cc_start: 0.6477 (t) cc_final: 0.6248 (t) REVERT: E 122 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8100 (t80) REVERT: R 172 PHE cc_start: 0.7024 (t80) cc_final: 0.6385 (t80) REVERT: R 306 MET cc_start: 0.8627 (mmm) cc_final: 0.8375 (mmt) REVERT: R 405 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6105 (mp10) outliers start: 39 outliers final: 26 residues processed: 153 average time/residue: 0.2407 time to fit residues: 51.4724 Evaluate side-chains 145 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.191393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.150084 restraints weight = 10117.198| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.43 r_work: 0.3405 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10209 Z= 0.099 Angle : 0.456 9.613 13866 Z= 0.242 Chirality : 0.040 0.230 1537 Planarity : 0.003 0.049 1768 Dihedral : 4.385 55.365 1400 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.33 % Allowed : 19.03 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.24), residues: 1248 helix: 2.55 (0.23), residues: 506 sheet: 0.42 (0.33), residues: 230 loop : -0.28 (0.28), residues: 512 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 0.011 0.001 PHE A 212 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 0.00161 ( 1) link_NAG-ASN : angle 0.68151 ( 3) hydrogen bonds : bond 0.03334 ( 515) hydrogen bonds : angle 3.91246 ( 1497) SS BOND : bond 0.00138 ( 9) SS BOND : angle 0.78784 ( 18) covalent geometry : bond 0.00214 (10198) covalent geometry : angle 0.45572 (13845) Misc. bond : bond 0.00057 ( 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 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7620 (t0) cc_final: 0.7070 (t70) REVERT: B 10 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: B 219 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6832 (mtm180) REVERT: E 93 PHE cc_start: 0.8371 (m-80) cc_final: 0.8021 (m-80) REVERT: E 122 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (t80) REVERT: R 172 PHE cc_start: 0.7122 (t80) cc_final: 0.6446 (t80) REVERT: R 221 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6781 (mp) REVERT: R 306 MET cc_start: 0.8569 (mmm) cc_final: 0.8308 (mmt) outliers start: 35 outliers final: 24 residues processed: 151 average time/residue: 0.2387 time to fit residues: 50.6233 Evaluate side-chains 147 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU 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: 8.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134895 restraints weight = 10370.653| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.63 r_work: 0.3230 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 10209 Z= 0.362 Angle : 0.745 10.207 13866 Z= 0.392 Chirality : 0.051 0.243 1537 Planarity : 0.006 0.052 1768 Dihedral : 5.338 55.034 1400 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.95 % Allowed : 18.27 % Favored : 76.78 % 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: 0.59 (0.24), residues: 1248 helix: 1.67 (0.23), residues: 506 sheet: -0.08 (0.32), residues: 248 loop : -0.64 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP N 47 HIS 0.010 0.002 HIS A 357 PHE 0.030 0.003 PHE N 108 TYR 0.018 0.003 TYR N 115 ARG 0.006 0.001 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 1.51408 ( 3) hydrogen bonds : bond 0.05410 ( 515) hydrogen bonds : angle 4.75279 ( 1497) SS BOND : bond 0.00528 ( 9) SS BOND : angle 3.12673 ( 18) covalent geometry : bond 0.00878 (10198) covalent geometry : angle 0.73639 (13845) Misc. bond : bond 0.00063 ( 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 184 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: B 59 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7842 (t80) REVERT: B 219 ARG cc_start: 0.7147 (mtm110) cc_final: 0.6854 (mtm180) REVERT: N 38 ARG cc_start: 0.8444 (ptt180) cc_final: 0.8182 (ptt90) REVERT: N 63 SER cc_start: 0.9123 (t) cc_final: 0.8769 (p) REVERT: E 93 PHE cc_start: 0.8578 (m-80) cc_final: 0.8122 (m-80) REVERT: E 122 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (t80) REVERT: R 172 PHE cc_start: 0.7205 (t80) cc_final: 0.6507 (t80) REVERT: R 221 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7115 (mp) REVERT: R 306 MET cc_start: 0.8858 (mmm) cc_final: 0.8607 (mmt) REVERT: R 397 GLU cc_start: 0.6984 (mp0) cc_final: 0.6758 (mp0) REVERT: R 405 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6374 (mp10) outliers start: 52 outliers final: 41 residues processed: 168 average time/residue: 0.2408 time to fit residues: 55.7888 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 270 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 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 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 SER 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 147 VAL 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 221 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.186021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141491 restraints weight = 10287.964| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.65 r_work: 0.3310 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10209 Z= 0.127 Angle : 0.517 9.675 13866 Z= 0.274 Chirality : 0.041 0.231 1537 Planarity : 0.004 0.054 1768 Dihedral : 4.895 55.475 1400 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 20.08 % Favored : 76.59 % 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: 0.95 (0.24), residues: 1248 helix: 2.15 (0.23), residues: 507 sheet: -0.19 (0.31), residues: 259 loop : -0.50 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.001 PHE B 241 TYR 0.015 0.001 TYR N 60 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 0.86104 ( 3) hydrogen bonds : bond 0.03856 ( 515) hydrogen bonds : angle 4.24753 ( 1497) SS BOND : bond 0.00260 ( 9) SS BOND : angle 1.84832 ( 18) covalent geometry : bond 0.00285 (10198) covalent geometry : angle 0.51258 (13845) Misc. bond : bond 0.00045 ( 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 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.161 Fit side-chains REVERT: B 10 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: B 59 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7756 (t80) REVERT: B 219 ARG cc_start: 0.7118 (mtm110) cc_final: 0.6798 (mtm180) REVERT: G 42 GLU cc_start: 0.7259 (pt0) cc_final: 0.6393 (mt-10) REVERT: N 63 SER cc_start: 0.9091 (t) cc_final: 0.8730 (p) REVERT: N 68 PHE cc_start: 0.7754 (m-10) cc_final: 0.7540 (m-10) REVERT: N 80 TYR cc_start: 0.8044 (m-80) cc_final: 0.7720 (m-80) REVERT: E 93 PHE cc_start: 0.8576 (m-80) cc_final: 0.8248 (m-80) REVERT: E 122 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8149 (t80) REVERT: R 172 PHE cc_start: 0.7187 (t80) cc_final: 0.6520 (t80) REVERT: R 199 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7084 (mt) REVERT: R 221 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7126 (mt) REVERT: R 306 MET cc_start: 0.8662 (mmm) cc_final: 0.8408 (mmt) REVERT: R 316 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7980 (tp) REVERT: R 405 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6365 (mp10) outliers start: 35 outliers final: 25 residues processed: 164 average time/residue: 0.2300 time to fit residues: 52.9877 Evaluate side-chains 162 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 221 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 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: 0.6980 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.187296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143546 restraints weight = 10324.134| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.50 r_work: 0.3362 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2869 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= 0.116 Angle : 0.496 9.619 13866 Z= 0.263 Chirality : 0.041 0.231 1537 Planarity : 0.004 0.053 1768 Dihedral : 4.729 55.605 1400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.71 % Allowed : 19.70 % Favored : 76.59 % 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: 1.10 (0.24), residues: 1248 helix: 2.31 (0.23), residues: 507 sheet: -0.11 (0.32), residues: 250 loop : -0.46 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE B 199 TYR 0.014 0.001 TYR N 60 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 0.71269 ( 3) hydrogen bonds : bond 0.03586 ( 515) hydrogen bonds : angle 4.10692 ( 1497) SS BOND : bond 0.00259 ( 9) SS BOND : angle 1.24443 ( 18) covalent geometry : bond 0.00262 (10198) covalent geometry : angle 0.49444 (13845) Misc. bond : bond 0.00045 ( 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 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.982 Fit side-chains REVERT: A 274 ASP cc_start: 0.7576 (t0) cc_final: 0.7353 (t0) REVERT: B 10 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: B 59 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 138 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 219 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6788 (mtm180) REVERT: G 42 GLU cc_start: 0.7216 (pt0) cc_final: 0.6390 (mt-10) REVERT: N 63 SER cc_start: 0.9068 (t) cc_final: 0.8707 (p) REVERT: N 105 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7401 (mtp-110) REVERT: E 83 PHE cc_start: 0.4561 (OUTLIER) cc_final: 0.4350 (t80) REVERT: E 93 PHE cc_start: 0.8535 (m-80) cc_final: 0.8198 (m-80) REVERT: E 122 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8037 (t80) REVERT: R 172 PHE cc_start: 0.7086 (t80) cc_final: 0.6435 (t80) REVERT: R 221 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7155 (mt) REVERT: R 306 MET cc_start: 0.8569 (mmm) cc_final: 0.8307 (mmt) REVERT: R 316 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7976 (tp) REVERT: R 405 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6431 (mp10) outliers start: 39 outliers final: 28 residues processed: 163 average time/residue: 0.2450 time to fit residues: 56.6202 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain B residue 228 ASP 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 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 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 221 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 347 ILE 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 43 optimal weight: 0.1980 chunk 79 optimal weight: 40.0000 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.188731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143782 restraints weight = 10248.650| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.57 r_work: 0.3384 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10209 Z= 0.103 Angle : 0.474 9.609 13866 Z= 0.250 Chirality : 0.040 0.233 1537 Planarity : 0.004 0.054 1768 Dihedral : 4.566 57.459 1400 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.14 % Allowed : 20.55 % 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: 1.25 (0.24), residues: 1248 helix: 2.45 (0.23), residues: 507 sheet: 0.01 (0.32), residues: 244 loop : -0.42 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 332 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR N 60 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 0.67391 ( 3) hydrogen bonds : bond 0.03315 ( 515) hydrogen bonds : angle 3.95039 ( 1497) SS BOND : bond 0.00449 ( 9) SS BOND : angle 1.21199 ( 18) covalent geometry : bond 0.00224 (10198) covalent geometry : angle 0.47253 (13845) Misc. bond : bond 0.00045 ( 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 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.005 Fit side-chains REVERT: B 10 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: B 59 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7660 (t80) REVERT: B 138 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 219 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6763 (mtm180) REVERT: G 42 GLU cc_start: 0.7194 (pt0) cc_final: 0.6385 (mt-10) REVERT: N 57 SER cc_start: 0.7696 (t) cc_final: 0.7495 (m) REVERT: E 83 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.4445 (t80) REVERT: E 93 PHE cc_start: 0.8558 (m-80) cc_final: 0.8207 (m-80) REVERT: E 122 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8000 (t80) REVERT: R 172 PHE cc_start: 0.7086 (t80) cc_final: 0.6448 (t80) REVERT: R 221 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7111 (mt) REVERT: R 306 MET cc_start: 0.8541 (mmm) cc_final: 0.8259 (mmt) REVERT: R 316 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7957 (tp) REVERT: R 405 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6442 (mp10) outliers start: 33 outliers final: 26 residues processed: 153 average time/residue: 0.2276 time to fit residues: 48.2681 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 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 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 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 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 164 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139822 restraints weight = 10289.156| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.54 r_work: 0.3328 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10209 Z= 0.172 Angle : 0.541 9.653 13866 Z= 0.285 Chirality : 0.042 0.229 1537 Planarity : 0.004 0.052 1768 Dihedral : 4.717 55.454 1400 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.52 % Allowed : 20.55 % 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: 1.07 (0.24), residues: 1248 helix: 2.26 (0.23), residues: 507 sheet: -0.08 (0.31), residues: 248 loop : -0.49 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE N 68 TYR 0.012 0.001 TYR R 149 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 0.87911 ( 3) hydrogen bonds : bond 0.03931 ( 515) hydrogen bonds : angle 4.18081 ( 1497) SS BOND : bond 0.00312 ( 9) SS BOND : angle 1.31153 ( 18) covalent geometry : bond 0.00408 (10198) covalent geometry : angle 0.53967 (13845) Misc. bond : bond 0.00043 ( 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 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: B 59 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 219 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6805 (mtm180) REVERT: G 42 GLU cc_start: 0.7321 (pt0) cc_final: 0.6399 (mt-10) REVERT: N 63 SER cc_start: 0.9068 (t) cc_final: 0.8720 (p) REVERT: E 83 PHE cc_start: 0.4705 (OUTLIER) cc_final: 0.4487 (t80) REVERT: E 93 PHE cc_start: 0.8556 (m-80) cc_final: 0.8192 (m-80) REVERT: E 122 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8089 (t80) REVERT: R 172 PHE cc_start: 0.7169 (t80) cc_final: 0.6502 (t80) REVERT: R 221 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7225 (mp) REVERT: R 306 MET cc_start: 0.8666 (mmm) cc_final: 0.8404 (mmt) REVERT: R 316 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (tp) REVERT: R 405 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6531 (mp10) outliers start: 37 outliers final: 30 residues processed: 155 average time/residue: 0.2336 time to fit residues: 50.3563 Evaluate side-chains 164 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 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 221 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 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 405 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.186273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142488 restraints weight = 10249.284| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.49 r_work: 0.3346 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3064 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= 0.131 Angle : 0.504 9.642 13866 Z= 0.266 Chirality : 0.041 0.231 1537 Planarity : 0.004 0.054 1768 Dihedral : 4.606 55.594 1400 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.71 % Allowed : 20.65 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.24), residues: 1248 helix: 2.33 (0.23), residues: 507 sheet: -0.11 (0.31), residues: 250 loop : -0.44 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 332 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE N 68 TYR 0.013 0.001 TYR N 60 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 0.77652 ( 3) hydrogen bonds : bond 0.03665 ( 515) hydrogen bonds : angle 4.08859 ( 1497) SS BOND : bond 0.00267 ( 9) SS BOND : angle 1.14432 ( 18) covalent geometry : bond 0.00304 (10198) covalent geometry : angle 0.50270 (13845) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5973.99 seconds wall clock time: 105 minutes 2.01 seconds (6302.01 seconds total)